PDB Short entry for 3BTZ HEADER OXIDOREDUCTASE/DNA 31-DEC-07 3BTZ TITLE CRYSTAL STRUCTURE OF HUMAN ABH2 CROSS-LINKED TO DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, OXY DC1; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*GP*GP*TP*GP*AP*(2YR)P*AP*AP*TP*GP*CP*G)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*DTP*DCP*DGP*DCP*DAP*DTP*DTP*DAP*DTP*DCP*DAP*DCP*DC)-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 STRAIN: 12Q24.11; SOURCE 6 GENE: ALKBH2, ABH2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES KEYWDS PROTEIN/DNA INTERACTION, HUMAN DIOXYGENASE, CROSS-LINK, DNA REPAIR, KEYWDS 2 DNA DAMAGE, IRON, METAL-BINDING, NUCLEUS, OXIDOREDUCTASE, KEYWDS 3 OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.-G.YANG,C.YI,C.HE REVDAT 6 20-OCT-21 3BTZ 1 SEQADV LINK REVDAT 5 21-MAY-14 3BTZ 1 COMPND REMARK SEQRES HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 HETATM ATOM REVDAT 4 13-JUL-11 3BTZ 1 VERSN REVDAT 3 24-FEB-09 3BTZ 1 VERSN REVDAT 2 10-JUN-08 3BTZ 1 JRNL REVDAT 1 22-APR-08 3BTZ 0 JRNL AUTH C.G.YANG,C.YI,E.M.DUGUID,C.T.SULLIVAN,X.JIAN,P.A.RICE,C.HE JRNL TITL CRYSTAL STRUCTURES OF DNA/RNA REPAIR ENZYMES ALKB AND ABH2 JRNL TITL 2 BOUND TO DSDNA. JRNL REF NATURE V. 452 961 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18432238 JRNL DOI 10.1038/NATURE06889 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9626 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 522 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 664 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.4000 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.4950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1625 REMARK 3 NUCLEIC ACID ATOMS : 529 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.20000 REMARK 3 B22 (A**2) : -1.20000 REMARK 3 B33 (A**2) : 2.39000 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): 1.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.379 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.339 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 41.816 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2262 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3170 ; 1.428 ; 2.245 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 6.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;29.617 ;21.410 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 277 ;19.429 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1551 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 888 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1438 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.169 ; 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): 27 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.146 ; 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): 1022 ; 0.346 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1626 ; 0.642 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1574 ; 1.110 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1544 ; 1.927 ; 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 57 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8747 28.9889 17.4350 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: -0.5925 REMARK 3 T33: -0.0624 T12: -0.0502 REMARK 3 T13: -0.0449 T23: -0.1447 REMARK 3 L TENSOR REMARK 3 L11: 4.5097 L22: 5.5344 REMARK 3 L33: 4.6044 L12: -2.0618 REMARK 3 L13: 1.2594 L23: -0.3992 REMARK 3 S TENSOR REMARK 3 S11: 0.1622 S12: 0.4393 S13: -0.4507 REMARK 3 S21: -0.4022 S22: -0.1401 S23: 0.0910 REMARK 3 S31: 0.3309 S32: -0.4372 S33: -0.0221 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 1 B 13 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2319 43.7234 14.3142 REMARK 3 T TENSOR REMARK 3 T11: 0.0515 T22: -0.2858 REMARK 3 T33: 0.1791 T12: 0.0507 REMARK 3 T13: -0.0360 T23: -0.1593 REMARK 3 L TENSOR REMARK 3 L11: 4.9003 L22: 2.4648 REMARK 3 L33: 13.3738 L12: -1.5348 REMARK 3 L13: 0.3246 L23: -2.5952 REMARK 3 S TENSOR REMARK 3 S11: -0.0421 S12: 0.0722 S13: 0.4387 REMARK 3 S21: 0.1261 S22: 0.1829 S23: 0.7753 REMARK 3 S31: -0.8167 S32: -2.1339 S33: -0.1408 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 1 C 13 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8473 42.9092 16.9766 REMARK 3 T TENSOR REMARK 3 T11: -0.0452 T22: -0.0467 REMARK 3 T33: 0.2081 T12: 0.0082 REMARK 3 T13: -0.0220 T23: -0.1073 REMARK 3 L TENSOR REMARK 3 L11: 3.0182 L22: 2.1809 REMARK 3 L33: 15.4977 L12: 2.2181 REMARK 3 L13: -1.2398 L23: -2.9708 REMARK 3 S TENSOR REMARK 3 S11: 0.1047 S12: -0.0166 S13: 0.3882 REMARK 3 S21: -0.2968 S22: 0.0894 S23: 0.5347 REMARK 3 S31: -0.0454 S32: -0.7853 S33: -0.1941 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 3BTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045953. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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 : 10204 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.93800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 4000, 0.1M SODIUM CHLORIDE, REMARK 280 0.05M MAGNESIUM CHLORIDE, 0.1M CACODYLATE, 0.004M HEXAMMINE REMARK 280 COBALT(III) CHLORIDE, PH 6.5, VAPOR DIFFUSION, HANGING DROP 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 83.09900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.76150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.76150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.54950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.76150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.76150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.64850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.76150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.76150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.54950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.76150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.76150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 124.64850 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 83.09900 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: 3910 ANGSTROM**2 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 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 DA B 1 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2YR B 7 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DT B 10 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 10 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DT B 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG C 3 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES REMARK 500 DG C 3 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DG C 3 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC C 4 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT C 7 O4' - C1' - N1 ANGL. DEV. = 2.4 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 ALA A 97 20.94 -142.12 REMARK 500 PRO A 109 53.02 -61.70 REMARK 500 ARG A 110 -166.78 172.48 REMARK 500 SER A 125 49.17 27.86 REMARK 500 TRP A 134 154.35 -49.22 REMARK 500 PRO A 229 38.23 -95.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FD8 RELATED DB: PDB REMARK 900 E. COLI HOMOLOG REMARK 900 RELATED ID: 2IUW RELATED DB: PDB REMARK 900 HUMAN HOMOLOG REMARK 900 RELATED ID: 3BTX RELATED DB: PDB REMARK 900 RELATED ID: 3BTY RELATED DB: PDB REMARK 900 RELATED ID: 3BU0 RELATED DB: PDB REMARK 900 RELATED ID: 3BUC RELATED DB: PDB DBREF 3BTZ A 57 258 UNP Q6NS38 ALKB2_HUMAN 57 258 DBREF 3BTZ B 1 13 PDB 3BTZ 3BTZ 1 13 DBREF 3BTZ C 1 13 PDB 3BTZ 3BTZ 1 13 SEQADV 3BTZ SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3BTZ SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3BTZ CYS A 175 UNP Q6NS38 GLU 175 ENGINEERED MUTATION SEQADV 3BTZ SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQRES 1 A 202 TRP ARG HIS ILE ARG ALA GLU GLY LEU ASP SER SER TYR SEQRES 2 A 202 THR VAL LEU PHE GLY LYS ALA GLU ALA ASP GLU ILE PHE SEQRES 3 A 202 GLN GLU LEU GLU LYS GLU VAL GLU TYR PHE THR GLY ALA SEQRES 4 A 202 LEU ALA ARG VAL GLN VAL PHE GLY LYS TRP HIS SER VAL SEQRES 5 A 202 PRO ARG LYS GLN ALA THR TYR GLY ASP ALA GLY LEU THR SEQRES 6 A 202 TYR THR PHE SER GLY LEU THR LEU SER PRO LYS PRO TRP SEQRES 7 A 202 ILE PRO VAL LEU GLU ARG ILE ARG ASP HIS VAL SER GLY SEQRES 8 A 202 VAL THR GLY GLN THR PHE ASN PHE VAL LEU ILE ASN ARG SEQRES 9 A 202 TYR LYS ASP GLY SER ASP HIS ILE GLY GLU HIS ARG ASP SEQRES 10 A 202 ASP CYS ARG GLU LEU ALA PRO GLY SER PRO ILE ALA SER SEQRES 11 A 202 VAL SER PHE GLY ALA SER ARG ASP PHE VAL PHE ARG HIS SEQRES 12 A 202 LYS ASP SER ARG GLY LYS SER PRO SER ARG ARG VAL ALA SEQRES 13 A 202 VAL VAL ARG LEU PRO LEU ALA HIS GLY SER LEU LEU MET SEQRES 14 A 202 MET ASN HIS PRO THR ASN THR HIS TRP TYR HIS SER LEU SEQRES 15 A 202 PRO VAL ARG LYS LYS VAL LEU ALA PRO ARG VAL ASN LEU SEQRES 16 A 202 THR PHE ARG LYS ILE LEU LEU SEQRES 1 B 13 DA DG DG DT DG DA 2YR DA DA DT DG DC DG SEQRES 1 C 13 DT DC DG DC DA DT DT DA DT DC DA DC DC HET 2YR B 7 22 HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 HOH *4(H2 O) 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 HELIX 4 4 ASP A 201 ARG A 203 5 3 HELIX 5 5 PRO A 229 HIS A 233 1 5 SHEET 1 A 7 ARG A 58 ALA A 62 0 SHEET 2 A 7 LEU A 65 VAL A 71 -1 O TYR A 69 N ARG A 58 SHEET 3 A 7 SER A 222 MET A 226 -1 O LEU A 223 N THR A 70 SHEET 4 A 7 ILE A 184 GLY A 190 -1 N ILE A 184 O MET A 226 SHEET 5 A 7 ARG A 248 ARG A 254 -1 O LEU A 251 N VAL A 187 SHEET 6 A 7 PHE A 155 TYR A 161 -1 N ASN A 159 O ASN A 250 SHEET 7 A 7 LYS A 111 GLY A 116 -1 N ALA A 113 O ILE A 158 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 PHE A 124 0 SHEET 2 C 2 LEU A 127 LEU A 129 -1 O LEU A 127 N PHE A 124 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 175 S 2YR B 7 1555 1555 2.06 LINK O3' DA B 6 P 2YR B 7 1555 1555 1.61 LINK O3' 2YR B 7 P DA B 8 1555 1555 1.61 CISPEP 1 HIS A 228 PRO A 229 0 6.08 CRYST1 75.523 75.523 166.198 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 0.013241 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006017 0.00000