PDB Short entry for 4XDO HEADER OXIDOREDUCTASE 19-DEC-14 4XDO TITLE CRYSTAL STRUCTURE OF HUMAN KDM4C CATALYTIC DOMAIN WITH OGA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4C; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 10-347); COMPND 5 SYNONYM: GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN,GASC-1 COMPND 6 PROTEIN,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3C, COMPND 7 JUMONJI DOMAIN-CONTAINING PROTEIN 2C; COMPND 8 EC: 1.14.11.-; COMPND 9 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: KDM4C, GASC1, JHDM3C, JMJD2C, KIAA0780; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYSINE-SPECIFIC DEMETHYLASE 4C, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.K.SWINGER,P.A.BORIACK-SJODIN REVDAT 2 01-JUL-15 4XDO 1 JRNL REVDAT 1 25-MAR-15 4XDO 0 JRNL AUTH T.J.WIGLE,K.K.SWINGER,J.E.CAMPBELL,M.D.SCHOLLE,J.SHERRILL, JRNL AUTH 2 E.A.ADMIRAND,P.A.BORIACK-SJODIN,K.W.KUNTZ,R.CHESWORTH, JRNL AUTH 3 M.P.MOYER,M.P.SCOTT,R.A.COPELAND JRNL TITL A HIGH-THROUGHPUT MASS SPECTROMETRY ASSAY COUPLED WITH REDOX JRNL TITL 2 ACTIVITY TESTING REDUCES ARTIFACTS AND FALSE POSITIVES IN JRNL TITL 3 LYSINE DEMETHYLASE SCREENING. JRNL REF J BIOMOL SCREEN V. 20 810 2015 JRNL REFN ESSN 1552-454X JRNL PMID 25755264 JRNL DOI 10.1177/1087057115575689 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54401 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2906 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 224 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5548 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.02000 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): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.405 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5839 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5408 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7889 ; 1.900 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12484 ; 0.916 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 688 ; 6.615 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 284 ;35.167 ;23.697 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 994 ;15.418 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;14.864 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 795 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6557 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1424 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2725 ; 2.214 ; 2.251 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2724 ; 2.213 ; 2.250 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3410 ; 3.193 ; 3.365 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4XDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205491. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57310 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 40.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M LITHIUM CHLORIDE, 0.1 M TRIS PH REMARK 280 8.5, 28 % W/V PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 46.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.96500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.88500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 OH TYR B 201 O HOH B 611 1.94 REMARK 500 OD2 ASP A 320 O HOH A 727 1.96 REMARK 500 O HOH A 619 O HOH A 706 2.03 REMARK 500 O HOH B 532 O HOH B 537 2.08 REMARK 500 O LEU B 68 O HOH B 637 2.11 REMARK 500 O HOH A 520 O HOH A 553 2.11 REMARK 500 NH2 ARG B 27 O HOH B 501 2.19 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 112 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP B 115 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP B 329 CB - CG - OD1 ANGL. DEV. = 6.1 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 PHE A 129 -124.53 -93.62 REMARK 500 ARG A 154 79.21 -156.41 REMARK 500 LYS A 184 1.53 85.58 REMARK 500 SER B 81 49.59 37.09 REMARK 500 PHE B 129 -122.61 -99.35 REMARK 500 ARG B 154 74.34 -160.70 REMARK 500 ASN B 156 70.64 59.74 REMARK 500 THR B 157 -161.08 -114.77 REMARK 500 GLU B 171 19.36 54.21 REMARK 500 LYS B 184 2.01 83.35 REMARK 500 ALA B 238 43.92 -108.47 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 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 190 NE2 REMARK 620 2 GLU A 192 OE2 94.1 REMARK 620 3 HIS A 278 NE2 87.7 97.1 REMARK 620 4 OGA A 403 O2' 94.9 167.9 91.3 REMARK 620 5 HOH A 568 O 95.9 84.2 176.0 86.8 REMARK 620 6 OGA A 403 O2 173.8 90.7 95.6 79.8 80.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 236 SG REMARK 620 2 HIS A 242 NE2 108.7 REMARK 620 3 CYS A 308 SG 116.0 113.6 REMARK 620 4 CYS A 310 SG 112.0 93.7 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 190 NE2 REMARK 620 2 GLU B 192 OE1 91.6 REMARK 620 3 HIS B 278 NE2 86.2 97.6 REMARK 620 4 OGA B 403 O2 176.4 90.7 96.3 REMARK 620 5 OGA B 403 O2' 94.4 161.9 99.8 82.7 REMARK 620 6 HOH B 543 O 88.2 83.2 174.3 89.3 80.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 236 SG REMARK 620 2 HIS B 242 NE2 109.5 REMARK 620 3 CYS B 308 SG 119.3 106.0 REMARK 620 4 CYS B 310 SG 111.9 102.3 106.4 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XML RELATED DB: PDB REMARK 900 RELATED ID: 4XDP RELATED DB: PDB DBREF 4XDO A 10 347 UNP Q9H3R0 KDM4C_HUMAN 10 347 DBREF 4XDO B 10 347 UNP Q9H3R0 KDM4C_HUMAN 10 347 SEQRES 1 A 338 LEU ASN PRO SER CYS LYS ILE MET THR PHE ARG PRO SER SEQRES 2 A 338 MET GLU GLU PHE ARG GLU PHE ASN LYS TYR LEU ALA TYR SEQRES 3 A 338 MET GLU SER LYS GLY ALA HIS ARG ALA GLY LEU ALA LYS SEQRES 4 A 338 VAL ILE PRO PRO LYS GLU TRP LYS PRO ARG GLN CYS TYR SEQRES 5 A 338 ASP ASP ILE ASP ASN LEU LEU ILE PRO ALA PRO ILE GLN SEQRES 6 A 338 GLN MET VAL THR GLY GLN SER GLY LEU PHE THR GLN TYR SEQRES 7 A 338 ASN ILE GLN LYS LYS ALA MET THR VAL LYS GLU PHE ARG SEQRES 8 A 338 GLN LEU ALA ASN SER GLY LYS TYR CYS THR PRO ARG TYR SEQRES 9 A 338 LEU ASP TYR GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN SEQRES 10 A 338 LEU THR PHE VAL ALA PRO ILE TYR GLY ALA ASP ILE ASN SEQRES 11 A 338 GLY SER ILE TYR ASP GLU GLY VAL ASP GLU TRP ASN ILE SEQRES 12 A 338 ALA ARG LEU ASN THR VAL LEU ASP VAL VAL GLU GLU GLU SEQRES 13 A 338 CYS GLY ILE SER ILE GLU GLY VAL ASN THR PRO TYR LEU SEQRES 14 A 338 TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR SEQRES 15 A 338 GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS PHE SEQRES 16 A 338 GLY GLU PRO LYS SER TRP TYR ALA ILE PRO PRO GLU HIS SEQRES 17 A 338 GLY LYS ARG LEU GLU ARG LEU ALA GLN GLY PHE PHE PRO SEQRES 18 A 338 SER SER SER GLN GLY CYS ASP ALA PHE LEU ARG HIS LYS SEQRES 19 A 338 MET THR LEU ILE SER PRO SER VAL LEU LYS LYS TYR GLY SEQRES 20 A 338 ILE PRO PHE ASP LYS ILE THR GLN GLU ALA GLY GLU PHE SEQRES 21 A 338 MET ILE THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN SEQRES 22 A 338 HIS GLY PHE ASN CYS ALA GLU SER THR ASN PHE ALA THR SEQRES 23 A 338 VAL ARG TRP ILE ASP TYR GLY LYS VAL ALA LYS LEU CYS SEQRES 24 A 338 THR CYS ARG LYS ASP MET VAL LYS ILE SER MET ASP ILE SEQRES 25 A 338 PHE VAL ARG LYS PHE GLN PRO ASP ARG TYR GLN LEU TRP SEQRES 26 A 338 LYS GLN GLY LYS ASP ILE TYR THR ILE ASP HIS THR LYS SEQRES 1 B 338 LEU ASN PRO SER CYS LYS ILE MET THR PHE ARG PRO SER SEQRES 2 B 338 MET GLU GLU PHE ARG GLU PHE ASN LYS TYR LEU ALA TYR SEQRES 3 B 338 MET GLU SER LYS GLY ALA HIS ARG ALA GLY LEU ALA LYS SEQRES 4 B 338 VAL ILE PRO PRO LYS GLU TRP LYS PRO ARG GLN CYS TYR SEQRES 5 B 338 ASP ASP ILE ASP ASN LEU LEU ILE PRO ALA PRO ILE GLN SEQRES 6 B 338 GLN MET VAL THR GLY GLN SER GLY LEU PHE THR GLN TYR SEQRES 7 B 338 ASN ILE GLN LYS LYS ALA MET THR VAL LYS GLU PHE ARG SEQRES 8 B 338 GLN LEU ALA ASN SER GLY LYS TYR CYS THR PRO ARG TYR SEQRES 9 B 338 LEU ASP TYR GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN SEQRES 10 B 338 LEU THR PHE VAL ALA PRO ILE TYR GLY ALA ASP ILE ASN SEQRES 11 B 338 GLY SER ILE TYR ASP GLU GLY VAL ASP GLU TRP ASN ILE SEQRES 12 B 338 ALA ARG LEU ASN THR VAL LEU ASP VAL VAL GLU GLU GLU SEQRES 13 B 338 CYS GLY ILE SER ILE GLU GLY VAL ASN THR PRO TYR LEU SEQRES 14 B 338 TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS THR SEQRES 15 B 338 GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS PHE SEQRES 16 B 338 GLY GLU PRO LYS SER TRP TYR ALA ILE PRO PRO GLU HIS SEQRES 17 B 338 GLY LYS ARG LEU GLU ARG LEU ALA GLN GLY PHE PHE PRO SEQRES 18 B 338 SER SER SER GLN GLY CYS ASP ALA PHE LEU ARG HIS LYS SEQRES 19 B 338 MET THR LEU ILE SER PRO SER VAL LEU LYS LYS TYR GLY SEQRES 20 B 338 ILE PRO PHE ASP LYS ILE THR GLN GLU ALA GLY GLU PHE SEQRES 21 B 338 MET ILE THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN SEQRES 22 B 338 HIS GLY PHE ASN CYS ALA GLU SER THR ASN PHE ALA THR SEQRES 23 B 338 VAL ARG TRP ILE ASP TYR GLY LYS VAL ALA LYS LEU CYS SEQRES 24 B 338 THR CYS ARG LYS ASP MET VAL LYS ILE SER MET ASP ILE SEQRES 25 B 338 PHE VAL ARG LYS PHE GLN PRO ASP ARG TYR GLN LEU TRP SEQRES 26 B 338 LYS GLN GLY LYS ASP ILE TYR THR ILE ASP HIS THR LYS HET ZN A 401 1 HET FE A 402 1 HET OGA A 403 10 HET PGE A 404 10 HET EDO A 405 4 HET PGE A 406 10 HET ZN B 401 1 HET FE B 402 1 HET OGA B 403 10 HET PG4 B 404 13 HETNAM ZN ZINC ION HETNAM FE FE (III) ION HETNAM OGA N-OXALYLGLYCINE HETNAM PGE TRIETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 FE 2(FE 3+) FORMUL 5 OGA 2(C4 H5 N O5) FORMUL 6 PGE 2(C6 H14 O4) FORMUL 7 EDO C2 H6 O2 FORMUL 12 PG4 C8 H18 O5 FORMUL 13 HOH *377(H2 O) HELIX 1 AA1 SER A 22 ARG A 27 1 6 HELIX 2 AA2 GLU A 28 LYS A 39 1 12 HELIX 3 AA3 GLY A 40 ALA A 44 5 5 HELIX 4 AA4 TYR A 61 ASN A 66 5 6 HELIX 5 AA5 VAL A 96 SER A 105 1 10 HELIX 6 AA6 ASP A 115 LEU A 127 1 13 HELIX 7 AA7 THR A 157 GLY A 167 1 11 HELIX 8 AA8 GLU A 192 LEU A 196 5 5 HELIX 9 AA9 PRO A 214 GLU A 216 5 3 HELIX 10 AB1 HIS A 217 PHE A 229 1 13 HELIX 11 AB2 PHE A 229 CYS A 236 1 8 HELIX 12 AB3 ALA A 238 LYS A 243 5 6 HELIX 13 AB4 SER A 248 TYR A 255 1 8 HELIX 14 AB5 ARG A 297 ALA A 305 1 9 HELIX 15 AB6 MET A 319 GLN A 327 1 9 HELIX 16 AB7 ARG A 330 GLN A 336 1 7 HELIX 17 AB8 SER B 22 ARG B 27 1 6 HELIX 18 AB9 GLU B 28 LYS B 39 1 12 HELIX 19 AC1 GLY B 40 ALA B 44 5 5 HELIX 20 AC2 TYR B 61 ASN B 66 5 6 HELIX 21 AC3 VAL B 96 SER B 105 1 10 HELIX 22 AC4 ASP B 115 LEU B 127 1 13 HELIX 23 AC5 THR B 157 GLY B 167 1 11 HELIX 24 AC6 GLU B 192 LEU B 196 5 5 HELIX 25 AC7 PRO B 214 GLU B 216 5 3 HELIX 26 AC8 HIS B 217 PHE B 229 1 13 HELIX 27 AC9 PHE B 229 CYS B 236 1 8 HELIX 28 AD1 ALA B 238 LYS B 243 5 6 HELIX 29 AD2 SER B 248 TYR B 255 1 8 HELIX 30 AD3 THR B 295 ARG B 297 5 3 HELIX 31 AD4 TRP B 298 ALA B 305 1 8 HELIX 32 AD5 MET B 319 GLN B 327 1 9 HELIX 33 AD6 ARG B 330 GLN B 336 1 7 SHEET 1 AA110 MET A 17 PHE A 19 0 SHEET 2 AA110 LEU A 46 VAL A 49 1 O LYS A 48 N MET A 17 SHEET 3 AA110 PHE A 269 THR A 272 -1 O PHE A 269 N VAL A 49 SHEET 4 AA110 TYR A 197 GLY A 205 -1 N ASN A 200 O MET A 270 SHEET 5 AA110 ASN A 286 PHE A 293 -1 O GLU A 289 N TYR A 201 SHEET 6 AA110 TYR A 177 GLY A 181 -1 N TYR A 179 O ALA A 288 SHEET 7 AA110 ILE A 133 ASN A 139 -1 N GLY A 135 O PHE A 180 SHEET 8 AA110 ILE A 73 GLN A 80 -1 N ILE A 73 O TYR A 134 SHEET 9 AA110 LEU A 83 GLN A 90 -1 O THR A 85 N THR A 78 SHEET 10 AA110 THR A 245 ILE A 247 -1 O LEU A 246 N PHE A 84 SHEET 1 AA2 2 LEU A 68 ILE A 69 0 SHEET 2 AA2 2 MET A 94 THR A 95 -1 O MET A 94 N ILE A 69 SHEET 1 AA3 4 THR A 186 HIS A 190 0 SHEET 2 AA3 4 TYR A 277 ASN A 282 -1 O GLY A 280 N PHE A 187 SHEET 3 AA3 4 LYS A 208 ILE A 213 -1 N TYR A 211 O ALA A 279 SHEET 4 AA3 4 ASP A 260 GLN A 264 -1 O GLN A 264 N LYS A 208 SHEET 1 AA410 MET B 17 PHE B 19 0 SHEET 2 AA410 LEU B 46 VAL B 49 1 O LYS B 48 N MET B 17 SHEET 3 AA410 PHE B 269 THR B 272 -1 O PHE B 269 N VAL B 49 SHEET 4 AA410 TYR B 197 GLY B 205 -1 N ASN B 200 O MET B 270 SHEET 5 AA410 ASN B 286 PHE B 293 -1 O GLU B 289 N TYR B 201 SHEET 6 AA410 TYR B 177 GLY B 181 -1 N TYR B 177 O SER B 290 SHEET 7 AA410 ILE B 133 ASN B 139 -1 N GLY B 135 O PHE B 180 SHEET 8 AA410 ILE B 73 GLN B 80 -1 N ILE B 73 O TYR B 134 SHEET 9 AA410 LEU B 83 GLN B 90 -1 O THR B 85 N THR B 78 SHEET 10 AA410 THR B 245 ILE B 247 -1 O LEU B 246 N PHE B 84 SHEET 1 AA5 2 LEU B 68 ILE B 69 0 SHEET 2 AA5 2 MET B 94 THR B 95 -1 O MET B 94 N ILE B 69 SHEET 1 AA6 4 THR B 186 HIS B 190 0 SHEET 2 AA6 4 TYR B 277 ASN B 282 -1 O GLY B 280 N PHE B 187 SHEET 3 AA6 4 LYS B 208 ILE B 213 -1 N SER B 209 O PHE B 281 SHEET 4 AA6 4 ASP B 260 GLN B 264 -1 O ILE B 262 N TRP B 210 LINK NE2 HIS A 190 FE FE A 402 1555 1555 2.12 LINK OE2 GLU A 192 FE FE A 402 1555 1555 2.03 LINK SG CYS A 236 ZN ZN A 401 1555 1555 2.25 LINK NE2 HIS A 242 ZN ZN A 401 1555 1555 2.13 LINK NE2 HIS A 278 FE FE A 402 1555 1555 2.07 LINK SG CYS A 308 ZN ZN A 401 1555 1555 2.24 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.37 LINK NE2 HIS B 190 FE FE B 402 1555 1555 2.03 LINK OE1 GLU B 192 FE FE B 402 1555 1555 1.89 LINK SG CYS B 236 ZN ZN B 401 1555 1555 2.31 LINK NE2 HIS B 242 ZN ZN B 401 1555 1555 2.15 LINK NE2 HIS B 278 FE FE B 402 1555 1555 2.13 LINK SG CYS B 308 ZN ZN B 401 1555 1555 2.16 LINK SG CYS B 310 ZN ZN B 401 1555 1555 2.35 LINK FE FE A 402 O2' OGA A 403 1555 1555 2.01 LINK FE FE A 402 O HOH A 568 1555 1555 2.09 LINK FE FE A 402 O2 OGA A 403 1555 1555 2.25 LINK FE FE B 402 O2 OGA B 403 1555 1555 2.06 LINK FE FE B 402 O2' OGA B 403 1555 1555 2.17 LINK FE FE B 402 O HOH B 543 1555 1555 2.21 SITE 1 AC1 4 CYS A 236 HIS A 242 CYS A 308 CYS A 310 SITE 1 AC2 5 HIS A 190 GLU A 192 HIS A 278 OGA A 403 SITE 2 AC2 5 HOH A 568 SITE 1 AC3 11 TYR A 134 TYR A 179 PHE A 187 HIS A 190 SITE 2 AC3 11 GLU A 192 SER A 198 ASN A 200 LYS A 208 SITE 3 AC3 11 HIS A 278 FE A 402 HOH A 568 SITE 1 AC4 3 ASP A 63 LEU A 67 ILE A 142 SITE 1 AC5 1 GLN A 90 SITE 1 AC6 4 CYS B 236 HIS B 242 CYS B 308 CYS B 310 SITE 1 AC7 5 HIS B 190 GLU B 192 HIS B 278 OGA B 403 SITE 2 AC7 5 HOH B 543 SITE 1 AC8 9 TYR B 134 HIS B 190 GLU B 192 SER B 198 SITE 2 AC8 9 ASN B 200 LYS B 208 HIS B 278 FE B 402 SITE 3 AC8 9 HOH B 543 SITE 1 AC9 3 ASP B 63 LEU B 67 SER B 141 CRYST1 93.930 89.770 98.460 90.00 96.49 90.00 C 1 2 1 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 0.010646 0.000000 0.001211 0.00000 SCALE2 0.000000 0.011140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010222 0.00000