PDB Short entry for 3RZM HEADER OXIDOREDUCTASE/DNA 11-MAY-11 3RZM TITLE DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN THE SEARCH OF TITLE 2 DAMAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-260; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, OXY DC1; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*AP*TP*GP*TP*AP*TP*AP*AP*CP*TP*GP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*TP*AP*CP*A)-3'; COMPND 15 CHAIN: C; COMPND 16 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: ALKBH2, ABH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, JELLY-ROLL, DEMETHYLASE, NUCLEUS, KEYWDS 2 OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,B.CHEN,B.QI,W.ZHANG,G.JIA,L.ZHANG,C.LI,A.DINNER,C.YANG,C.HE REVDAT 3 01-NOV-23 3RZM 1 REMARK SEQADV LINK REVDAT 2 03-JUL-13 3RZM 1 JRNL REVDAT 1 06-JUN-12 3RZM 0 JRNL AUTH C.YI,B.CHEN,B.QI,W.ZHANG,G.JIA,L.ZHANG,C.J.LI,A.R.DINNER, JRNL AUTH 2 C.G.YANG,C.HE JRNL TITL DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN JRNL TITL 2 SEARCH OF BASE DAMAGE JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 671 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22659876 JRNL DOI 10.1038/NSMB.2320 REMARK 2 REMARK 2 RESOLUTION. 3.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.200 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9236 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 469 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) : 3.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 657 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1614 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 2.12000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.434 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.362 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.402 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2258 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3165 ; 1.255 ; 2.242 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 199 ; 6.809 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;31.161 ;21.646 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;18.993 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.698 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1545 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1002 ; 0.431 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1617 ; 0.801 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1256 ; 0.874 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1548 ; 1.628 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 55 A 260 REMARK 3 ORIGIN FOR THE GROUP (A): 21.8171 -1.8038 18.2493 REMARK 3 T TENSOR REMARK 3 T11: 0.4984 T22: 0.0374 REMARK 3 T33: 0.1102 T12: 0.0542 REMARK 3 T13: 0.0447 T23: 0.0377 REMARK 3 L TENSOR REMARK 3 L11: 4.0451 L22: 4.6016 REMARK 3 L33: 1.3830 L12: 1.0015 REMARK 3 L13: -1.3658 L23: 1.0836 REMARK 3 S TENSOR REMARK 3 S11: -0.1203 S12: -0.2243 S13: -0.1378 REMARK 3 S21: 0.4121 S22: 0.1584 S23: -0.0717 REMARK 3 S31: 0.1499 S32: 0.2014 S33: -0.0382 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 261 B 273 REMARK 3 ORIGIN FOR THE GROUP (A): 40.329 7.716 25.436 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.2737 REMARK 3 T33: 0.2737 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 274 C 286 REMARK 3 ORIGIN FOR THE GROUP (A): 40.220 7.547 23.407 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.2737 REMARK 3 T33: 0.2737 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3RZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.5 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-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9613 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.060 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 3BTX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 4000, 0.1M SODIUM CHLORIDE, REMARK 280 0.05M MAGNESIUM CHLORIDE, 0.1M CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 84.85500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.52500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.42750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.52500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.52500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 127.28250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.52500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.52500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.42750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.52500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.52500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 127.28250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.85500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 SER A 202 REMARK 465 ARG A 203 REMARK 465 GLY A 204 REMARK 465 LYS A 205 REMARK 465 SER A 206 REMARK 465 PRO A 207 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 HIS A 228 C PRO A 229 N 0.237 REMARK 500 PRO A 229 C THR A 230 N 0.224 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 PRO A 229 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PRO A 229 C - N - CD ANGL. DEV. = -25.9 DEGREES REMARK 500 PRO A 229 CA - C - N ANGL. DEV. = -27.0 DEGREES REMARK 500 PRO A 229 O - C - N ANGL. DEV. = 19.5 DEGREES REMARK 500 LEU A 258 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 DT B 262 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 262 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 262 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG B 271 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC B 272 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG C 276 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC C 277 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC C 277 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 279 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT C 280 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 283 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 285 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC C 285 O4' - C1' - N1 ANGL. DEV. = 4.5 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 PRO A 109 58.09 -66.71 REMARK 500 ARG A 110 -163.05 179.23 REMARK 500 ASP A 174 113.51 -36.40 REMARK 500 PRO A 229 144.08 0.24 REMARK 500 LEU A 258 -8.12 65.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XL3 B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RZG RELATED DB: PDB REMARK 900 RELATED ID: 3RZH RELATED DB: PDB REMARK 900 RELATED ID: 3RZJ RELATED DB: PDB REMARK 900 RELATED ID: 3RZK RELATED DB: PDB REMARK 900 RELATED ID: 3RZL RELATED DB: PDB DBREF 3RZM A 56 260 UNP Q6NS38 ALKB2_HUMAN 56 260 DBREF 3RZM B 261 273 PDB 3RZM 3RZM 261 273 DBREF 3RZM C 274 286 PDB 3RZM 3RZM 274 286 SEQADV 3RZM HIS A 55 UNP Q6NS38 EXPRESSION TAG SEQADV 3RZM SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3RZM SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3RZM CYS A 169 UNP Q6NS38 GLY 169 ENGINEERED MUTATION SEQADV 3RZM SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQADV 3RZM ALA A 260 UNP Q6NS38 LYS 260 ENGINEERED MUTATION SEQRES 1 A 206 HIS SER TRP ARG HIS ILE ARG ALA GLU GLY LEU ASP SER SEQRES 2 A 206 SER TYR THR VAL LEU PHE GLY LYS ALA GLU ALA ASP GLU SEQRES 3 A 206 ILE PHE GLN GLU LEU GLU LYS GLU VAL GLU TYR PHE THR SEQRES 4 A 206 GLY ALA LEU ALA ARG VAL GLN VAL PHE GLY LYS TRP HIS SEQRES 5 A 206 SER VAL PRO ARG LYS GLN ALA THR TYR GLY ASP ALA GLY SEQRES 6 A 206 LEU THR TYR THR PHE SER GLY LEU THR LEU SER PRO LYS SEQRES 7 A 206 PRO TRP ILE PRO VAL LEU GLU ARG ILE ARG ASP HIS VAL SEQRES 8 A 206 SER GLY VAL THR GLY GLN THR PHE ASN PHE VAL LEU ILE SEQRES 9 A 206 ASN ARG TYR LYS ASP GLY SER ASP HIS ILE CYS GLU HIS SEQRES 10 A 206 ARG ASP ASP GLU ARG GLU LEU ALA PRO GLY SER PRO ILE SEQRES 11 A 206 ALA SER VAL SER PHE GLY ALA SER ARG ASP PHE VAL PHE SEQRES 12 A 206 ARG HIS LYS ASP SER ARG GLY LYS SER PRO SER ARG ARG SEQRES 13 A 206 VAL ALA VAL VAL ARG LEU PRO LEU ALA HIS GLY SER LEU SEQRES 14 A 206 LEU MET MET ASN HIS PRO THR ASN THR HIS TRP TYR HIS SEQRES 15 A 206 SER LEU PRO VAL ARG LYS LYS VAL LEU ALA PRO ARG VAL SEQRES 16 A 206 ASN LEU THR PHE ARG LYS ILE LEU LEU THR ALA SEQRES 1 B 13 DA DT DG DT DA DT DA DA DC DT DG DC DG SEQRES 1 C 13 DT DC DG DC DA DG DT DT DA DT DA DC DA HET XL3 B 1 4 HETNAM XL3 PROPANE-1-THIOL FORMUL 4 XL3 C3 H8 S HELIX 1 1 GLY A 74 VAL A 89 1 16 HELIX 2 2 THR A 93 LEU A 96 5 4 HELIX 3 3 ILE A 135 GLY A 150 1 16 SHEET 1 A 7 TRP A 57 ALA A 62 0 SHEET 2 A 7 LEU A 65 VAL A 71 -1 O SER A 67 N ILE A 60 SHEET 3 A 7 SER A 222 ASN A 227 -1 O LEU A 223 N THR A 70 SHEET 4 A 7 PRO A 183 GLY A 190 -1 N SER A 186 O LEU A 224 SHEET 5 A 7 ARG A 248 ARG A 254 -1 O PHE A 253 N ALA A 185 SHEET 6 A 7 PHE A 155 TYR A 161 -1 N TYR A 161 O ARG A 248 SHEET 7 A 7 LYS A 111 GLY A 116 -1 N TYR A 115 O VAL A 156 SHEET 1 B 2 ARG A 98 VAL A 101 0 SHEET 2 B 2 LYS A 104 SER A 107 -1 O HIS A 106 N VAL A 99 SHEET 1 C 2 TYR A 122 THR A 123 0 SHEET 2 C 2 THR A 128 LEU A 129 -1 O LEU A 129 N TYR A 122 SHEET 1 D 4 ILE A 168 HIS A 171 0 SHEET 2 D 4 TRP A 234 LEU A 238 -1 O HIS A 236 N HIS A 171 SHEET 3 D 4 ARG A 193 HIS A 199 -1 N ARG A 198 O TYR A 235 SHEET 4 D 4 VAL A 214 LEU A 218 -1 O LEU A 216 N PHE A 195 LINK SG CYS A 169 SG XL3 B 1 1555 1555 2.05 LINK CA XL3 B 1 N4 DC B 269 1555 1555 1.48 SITE 1 AC1 2 CYS A 169 DC B 269 CRYST1 75.050 75.050 169.710 90.00 90.00 90.00 P 41 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 0.013324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005892 0.00000