PDB Short entry for 2Q8D HEADER OXIDOREDUCTASE 10-JUN-07 2Q8D TITLE CRYSTAL STRUCTURE OF JMJ2D2A IN TERNARY COMPLEX WITH HISTONE H3-K36ME2 TITLE 2 AND SUCCINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: JUMONJI DOMAIN; COMPND 5 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE 3 PEPTIDE; COMPND 10 CHAIN: F, G; COMPND 11 SYNONYM: PEPTIDE; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JMJD2A, JHDM3A, JMJD2, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS HISTONE DEMETHYLASE, HYDROXYLASE, SUCCINATE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-F.COUTURE,E.COLLAZO,P.ORTIZ-TELLO,J.S.BRUNZELLE,R.C.TRIEVEL REVDAT 5 30-AUG-23 2Q8D 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 2Q8D 1 AUTHOR REVDAT 3 24-FEB-09 2Q8D 1 VERSN REVDAT 2 29-JAN-08 2Q8D 1 JRNL REVDAT 1 03-JUL-07 2Q8D 0 JRNL AUTH J.F.COUTURE,E.COLLAZO,P.A.ORTIZ-TELLO,J.S.BRUNZELLE, JRNL AUTH 2 R.C.TRIEVEL JRNL TITL SPECIFICITY AND MECHANISM OF JMJD2A, A JRNL TITL 2 TRIMETHYLLYSINE-SPECIFIC HISTONE DEMETHYLASE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 689 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17589523 JRNL DOI 10.1038/NSMB1273 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 38402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1927 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2150 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.326 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.238 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.580 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5857 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7925 ; 1.294 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 690 ; 5.825 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 283 ;32.968 ;23.251 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 972 ;17.724 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.500 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 810 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4534 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2671 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3972 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 286 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.252 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3561 ; 0.539 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5599 ; 0.943 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2680 ; 1.408 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2326 ; 2.160 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2Q8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38447 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 37.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 REMARK 200 R SYM FOR SHELL (I) : 0.45200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2GP5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.42850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.32100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.42850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.32100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 566 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 PRO A 348 REMARK 465 GLU A 349 REMARK 465 ALA A 350 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 GLU B 6 REMARK 465 THR B 7 REMARK 465 LEU B 8 REMARK 465 THR B 347 REMARK 465 PRO B 348 REMARK 465 GLU B 349 REMARK 465 ALA B 350 REMARK 465 ARG F 26 REMARK 465 LYS F 27 REMARK 465 SER F 28 REMARK 465 ALA F 29 REMARK 465 PRO F 30 REMARK 465 ALA F 31 REMARK 465 THR F 32 REMARK 465 LYS F 37 REMARK 465 PRO F 38 REMARK 465 HIS F 39 REMARK 465 ARG F 40 REMARK 465 TYR F 41 REMARK 465 ARG G 26 REMARK 465 LYS G 27 REMARK 465 SER G 28 REMARK 465 ALA G 29 REMARK 465 PRO G 30 REMARK 465 ALA G 31 REMARK 465 LYS G 37 REMARK 465 PRO G 38 REMARK 465 HIS G 39 REMARK 465 ARG G 40 REMARK 465 TYR G 41 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 ARG A 29 CD NE CZ NH1 NH2 REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 99 CE NZ REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 221 CD NE CZ NH1 NH2 REMARK 470 LYS A 336 CD CE NZ REMARK 470 GLU B 22 CD OE1 OE2 REMARK 470 LYS B 54 CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 LYS B 310 CD CE NZ REMARK 470 LYS B 314 CD CE NZ REMARK 470 THR G 32 CB OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 510 O HOH B 594 1.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 95 CZ ARG B 95 NH1 0.087 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 95 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG B 95 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 152 71.87 -156.59 REMARK 500 MET A 192 18.27 58.01 REMARK 500 ALA A 236 59.31 -146.81 REMARK 500 ARG B 152 79.43 -163.05 REMARK 500 VAL B 171 -61.71 -95.21 REMARK 500 LYS B 182 5.10 83.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 101.0 REMARK 620 3 HIS A 276 NE2 83.9 76.8 REMARK 620 4 SIN A 503 O1 85.5 173.5 104.4 REMARK 620 5 SIN A 503 O2 137.6 120.6 111.9 53.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 105.1 REMARK 620 3 CYS A 306 SG 114.9 116.4 REMARK 620 4 CYS A 308 SG 108.0 98.0 112.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 502 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 98.7 REMARK 620 3 HIS B 276 NE2 89.0 80.9 REMARK 620 4 SIN B 504 O1 86.5 170.6 107.1 REMARK 620 5 SIN B 504 O2 139.9 120.9 102.2 53.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 109.1 REMARK 620 3 CYS B 306 SG 115.8 111.5 REMARK 620 4 CYS B 308 SG 114.1 90.1 113.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q8C RELATED DB: PDB REMARK 900 JMJD2A IN TERNARY COMPLEX IN HISTONE H3-K9ME3 AND 2-OXOGLUTARATE REMARK 900 RELATED ID: 2Q8E RELATED DB: PDB REMARK 900 SAME PROTEIN WITH N-OXALYLGLYCINE DBREF 2Q8D A 1 350 UNP O75164 JHD3A_HUMAN 1 350 DBREF 2Q8D B 1 350 UNP O75164 JHD3A_HUMAN 1 350 DBREF 2Q8D F 26 41 PDB 2Q8D 2Q8D 26 41 DBREF 2Q8D G 26 41 PDB 2Q8D 2Q8D 26 41 SEQADV 2Q8D GLY A -1 UNP O75164 CLONING ARTIFACT SEQADV 2Q8D SER A 0 UNP O75164 CLONING ARTIFACT SEQADV 2Q8D GLY B -1 UNP O75164 CLONING ARTIFACT SEQADV 2Q8D SER B 0 UNP O75164 CLONING ARTIFACT SEQRES 1 A 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 A 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 A 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 A 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 A 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 A 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 A 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 A 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 A 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 A 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 A 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 A 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 A 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 A 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 A 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 A 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 A 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 A 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 A 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 A 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 A 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 A 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 A 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 A 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 A 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 A 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 A 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 A 352 ALA SEQRES 1 B 352 GLY SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER SEQRES 2 B 352 ALA ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE SEQRES 3 B 352 ARG ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN SEQRES 4 B 352 GLY ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO SEQRES 5 B 352 LYS GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP SEQRES 6 B 352 ASP LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR SEQRES 7 B 352 GLY GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS SEQRES 8 B 352 LYS ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SEQRES 9 B 352 SER ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU SEQRES 10 B 352 GLU LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN SEQRES 11 B 352 PRO PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR SEQRES 12 B 352 GLU LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG SEQRES 13 B 352 THR ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR SEQRES 14 B 352 ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET SEQRES 15 B 352 TRP LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP SEQRES 16 B 352 LEU TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SEQRES 17 B 352 SER TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU SEQRES 18 B 352 GLU ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SEQRES 19 B 352 SER CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SEQRES 20 B 352 SER PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP SEQRES 21 B 352 LYS VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE SEQRES 22 B 352 PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN SEQRES 23 B 352 CYS ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE SEQRES 24 B 352 GLU TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS SEQRES 25 B 352 ASP MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS SEQRES 26 B 352 PHE GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS SEQRES 27 B 352 ASP ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU SEQRES 28 B 352 ALA SEQRES 1 F 16 ARG LYS SER ALA PRO ALA THR GLY GLY VAL MLY LYS PRO SEQRES 2 F 16 HIS ARG TYR SEQRES 1 G 16 ARG LYS SER ALA PRO ALA THR GLY GLY VAL MLY LYS PRO SEQRES 2 G 16 HIS ARG TYR MODRES 2Q8D MLY F 36 LYS N-DIMETHYL-LYSINE MODRES 2Q8D MLY G 36 LYS N-DIMETHYL-LYSINE HET MLY F 36 11 HET MLY G 36 11 HET NI A 501 1 HET ZN A 505 1 HET SIN A 503 8 HET NI B 502 1 HET ZN B 506 1 HET SIN B 504 8 HETNAM MLY N-DIMETHYL-LYSINE HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM SIN SUCCINIC ACID FORMUL 3 MLY 2(C8 H18 N2 O2) FORMUL 5 NI 2(NI 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 SIN 2(C4 H6 O4) FORMUL 11 HOH *224(H2 O) HELIX 1 1 SER A 3 LEU A 8 1 6 HELIX 2 2 THR A 20 ARG A 25 1 6 HELIX 3 3 ASN A 26 SER A 36 1 11 HELIX 4 4 GLY A 38 ALA A 42 5 5 HELIX 5 5 VAL A 94 SER A 103 1 10 HELIX 6 6 GLU A 113 LEU A 125 1 13 HELIX 7 7 THR A 155 LEU A 157 5 3 HELIX 8 8 ASP A 158 GLY A 165 1 8 HELIX 9 9 GLU A 190 LEU A 194 5 5 HELIX 10 10 PRO A 212 GLU A 214 5 3 HELIX 11 11 HIS A 215 PHE A 227 1 13 HELIX 12 12 PHE A 227 CYS A 234 1 8 HELIX 13 13 ALA A 236 LYS A 241 5 6 HELIX 14 14 SER A 246 TYR A 253 1 8 HELIX 15 15 ARG A 295 ALA A 303 1 9 HELIX 16 16 MET A 317 GLN A 325 1 9 HELIX 17 17 ARG A 328 ALA A 334 1 7 HELIX 18 18 ASN B 9 ARG B 13 5 5 HELIX 19 19 THR B 20 ARG B 25 1 6 HELIX 20 20 ASN B 26 GLN B 37 1 12 HELIX 21 21 GLY B 38 ALA B 42 5 5 HELIX 22 22 VAL B 94 SER B 103 1 10 HELIX 23 23 GLU B 113 LEU B 125 1 13 HELIX 24 24 THR B 155 LEU B 157 5 3 HELIX 25 25 ASP B 158 GLU B 163 1 6 HELIX 26 26 GLU B 190 LEU B 194 5 5 HELIX 27 27 PRO B 212 GLU B 214 5 3 HELIX 28 28 HIS B 215 PHE B 227 1 13 HELIX 29 29 PHE B 227 CYS B 234 1 8 HELIX 30 30 ALA B 236 LYS B 241 5 6 HELIX 31 31 SER B 246 TYR B 253 1 8 HELIX 32 32 ARG B 295 ALA B 303 1 9 HELIX 33 33 MET B 317 GLN B 325 1 9 HELIX 34 34 ARG B 328 GLY B 335 1 8 SHEET 1 A10 MET A 15 PHE A 17 0 SHEET 2 A10 LEU A 44 VAL A 47 1 O LYS A 46 N PHE A 17 SHEET 3 A10 PHE A 267 THR A 270 -1 O PHE A 267 N VAL A 47 SHEET 4 A10 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 A10 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 A10 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 A10 ILE A 131 ASN A 137 -1 N GLY A 133 O PHE A 178 SHEET 8 A10 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 A10 LEU A 81 GLN A 88 -1 O ILE A 87 N GLN A 72 SHEET 10 A10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 B 2 VAL A 66 ILE A 67 0 SHEET 2 B 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 C 4 SER A 184 HIS A 188 0 SHEET 2 C 4 TYR A 275 ASN A 280 -1 O GLY A 278 N PHE A 185 SHEET 3 C 4 LYS A 206 VAL A 211 -1 N TYR A 209 O ALA A 277 SHEET 4 C 4 ASP A 258 GLN A 262 -1 O VAL A 260 N TRP A 208 SHEET 1 D10 THR B 16 PHE B 17 0 SHEET 2 D10 LEU B 44 VAL B 47 1 O LYS B 46 N PHE B 17 SHEET 3 D10 PHE B 267 THR B 270 -1 O ILE B 269 N ALA B 45 SHEET 4 D10 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 D10 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 D10 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 D10 ILE B 131 ASN B 137 -1 N VAL B 136 O LEU B 176 SHEET 8 D10 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 D10 LEU B 81 GLN B 88 -1 O TYR B 85 N LEU B 74 SHEET 10 D10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 E 2 VAL B 66 ILE B 67 0 SHEET 2 E 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 F 4 SER B 184 HIS B 188 0 SHEET 2 F 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 F 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 F 4 ASP B 258 GLN B 262 -1 O GLN B 262 N LYS B 206 LINK C VAL F 35 N MLY F 36 1555 1555 1.34 LINK C VAL G 35 N MLY G 36 1555 1555 1.33 LINK NE2 HIS A 188 NI NI A 501 1555 1555 2.32 LINK OE1 GLU A 190 NI NI A 501 1555 1555 2.22 LINK SG CYS A 234 ZN ZN A 505 1555 1555 2.24 LINK NE2 HIS A 240 ZN ZN A 505 1555 1555 2.17 LINK NE2 HIS A 276 NI NI A 501 1555 1555 2.20 LINK SG CYS A 306 ZN ZN A 505 1555 1555 2.17 LINK SG CYS A 308 ZN ZN A 505 1555 1555 2.47 LINK NI NI A 501 O1 SIN A 503 1555 1555 2.33 LINK NI NI A 501 O2 SIN A 503 1555 1555 2.65 LINK NE2 HIS B 188 NI NI B 502 1555 1555 2.25 LINK OE1 GLU B 190 NI NI B 502 1555 1555 2.26 LINK SG CYS B 234 ZN ZN B 506 1555 1555 2.20 LINK NE2 HIS B 240 ZN ZN B 506 1555 1555 2.20 LINK NE2 HIS B 276 NI NI B 502 1555 1555 2.28 LINK SG CYS B 306 ZN ZN B 506 1555 1555 2.22 LINK SG CYS B 308 ZN ZN B 506 1555 1555 2.42 LINK NI NI B 502 O1 SIN B 504 1555 1555 2.26 LINK NI NI B 502 O2 SIN B 504 1555 1555 2.67 SITE 1 AC1 4 HIS A 188 GLU A 190 HIS A 276 SIN A 503 SITE 1 AC2 4 HIS B 188 GLU B 190 HIS B 276 SIN B 504 SITE 1 AC3 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC4 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC5 8 TYR A 132 PHE A 185 HIS A 188 ASN A 198 SITE 2 AC5 8 LYS A 206 HIS A 276 NI A 501 HOH A 574 SITE 1 AC6 9 TYR B 132 TYR B 177 PHE B 185 HIS B 188 SITE 2 AC6 9 ASN B 198 LYS B 206 TRP B 208 HIS B 276 SITE 3 AC6 9 NI B 502 CRYST1 100.857 148.642 57.346 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017438 0.00000