PDB Short entry for 3BU0 HEADER OXIDOREDUCTASE/DNA 31-DEC-07 3BU0 TITLE CRYSTAL STRUCTURE OF HUMAN ABH2 CROSS-LINKED TO DSDNA WITH COFACTORS 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(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*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*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-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, DNA REPAIR, CROSS-LINK, 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 3BU0 1 REMARK SEQADV LINK REVDAT 5 21-MAY-14 3BU0 1 COMPND REMARK SEQRES HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 HETATM ATOM REVDAT 4 13-JUL-11 3BU0 1 VERSN REVDAT 3 24-FEB-09 3BU0 1 VERSN REVDAT 2 10-JUN-08 3BU0 1 JRNL REVDAT 1 22-APR-08 3BU0 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13964 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 973 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.5220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1631 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 91 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) : 36.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33000 REMARK 3 B22 (A**2) : -1.33000 REMARK 3 B33 (A**2) : 2.00000 REMARK 3 B12 (A**2) : -0.67000 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): 0.397 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.291 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.199 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2275 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3186 ; 1.192 ; 2.246 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 5.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;26.203 ;21.410 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 278 ;13.548 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1569 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 886 ; 0.177 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1444 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 128 ; 0.120 ; 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): 32 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.130 ; 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): 1039 ; 0.351 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1636 ; 0.639 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1570 ; 0.916 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1550 ; 1.517 ; 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 56 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 109.7990 -2.6565-192.6304 REMARK 3 T TENSOR REMARK 3 T11: -0.0790 T22: -0.1376 REMARK 3 T33: -0.0130 T12: -0.0353 REMARK 3 T13: 0.1048 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 5.8551 L22: 3.4783 REMARK 3 L33: 2.0433 L12: -1.5350 REMARK 3 L13: -0.0684 L23: -0.4345 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: 0.3667 S13: -0.1712 REMARK 3 S21: -0.5766 S22: 0.1256 S23: -0.1760 REMARK 3 S31: 0.1646 S32: 0.0256 S33: -0.1723 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): 87.4783 2.2602-193.0706 REMARK 3 T TENSOR REMARK 3 T11: 0.1001 T22: 0.0077 REMARK 3 T33: -0.0275 T12: 0.0446 REMARK 3 T13: 0.0425 T23: 0.1739 REMARK 3 L TENSOR REMARK 3 L11: 3.8517 L22: 1.3467 REMARK 3 L33: 0.5669 L12: 2.2691 REMARK 3 L13: 1.1983 L23: 0.6619 REMARK 3 S TENSOR REMARK 3 S11: -0.1101 S12: -0.2949 S13: -0.1680 REMARK 3 S21: -0.1535 S22: 0.1735 S23: 0.2526 REMARK 3 S31: 0.0405 S32: -0.4227 S33: -0.0634 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): 89.6149 3.8984-192.4189 REMARK 3 T TENSOR REMARK 3 T11: 0.0009 T22: 0.1170 REMARK 3 T33: -0.0539 T12: -0.0984 REMARK 3 T13: -0.0127 T23: 0.0927 REMARK 3 L TENSOR REMARK 3 L11: 1.7720 L22: 2.7943 REMARK 3 L33: 19.2565 L12: -1.1312 REMARK 3 L13: 2.0608 L23: -7.1281 REMARK 3 S TENSOR REMARK 3 S11: -0.1298 S12: -0.2803 S13: -0.0155 REMARK 3 S21: -0.1022 S22: 0.4554 S23: 0.3009 REMARK 3 S31: -0.5108 S32: -0.6997 S33: -0.3256 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 3BU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045954. 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 : 6.1 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 : 14823 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 33.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 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 (%): 61.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 0.1M SODIUM CHLORIDE, REMARK 280 0.05M MAGNESIUM CHLORIDE, 0.1M CACODYLATE, 0.001M MNCL2, 0.002M REMARK 280 2-KETOGLUTARATE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 151.36733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.68367 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.52550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.84183 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 189.20917 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 151.36733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 75.68367 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 37.84183 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 113.52550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 189.20917 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: 4440 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 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 10 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 3.4 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 ARG A 110 -176.35 178.40 REMARK 500 LYS A 205 -70.64 -40.61 REMARK 500 ARG A 210 45.77 -109.09 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 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 171 NE2 REMARK 620 2 ASP A 173 OD1 83.1 REMARK 620 3 HIS A 236 NE2 89.1 98.8 REMARK 620 4 AKG A 301 O5 101.5 171.8 88.1 REMARK 620 5 AKG A 301 O2 80.6 99.4 157.9 75.0 REMARK 620 6 HOH A 451 O 168.8 101.0 100.4 73.3 88.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 302 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: 3BTZ RELATED DB: PDB REMARK 900 RELATED ID: 3BUC RELATED DB: PDB DBREF 3BU0 A 56 258 UNP Q6NS38 ALKB2_HUMAN 56 258 DBREF 3BU0 B 1 13 PDB 3BU0 3BU0 1 13 DBREF 3BU0 C 1 13 PDB 3BU0 3BU0 1 13 SEQADV 3BU0 SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3BU0 SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3BU0 CYS A 175 UNP Q6NS38 GLU 175 ENGINEERED MUTATION SEQADV 3BU0 SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQRES 1 A 203 SER TRP ARG HIS ILE ARG ALA GLU GLY LEU ASP SER SER SEQRES 2 A 203 TYR THR VAL LEU PHE GLY LYS ALA GLU ALA ASP GLU ILE SEQRES 3 A 203 PHE GLN GLU LEU GLU LYS GLU VAL GLU TYR PHE THR GLY SEQRES 4 A 203 ALA LEU ALA ARG VAL GLN VAL PHE GLY LYS TRP HIS SER SEQRES 5 A 203 VAL PRO ARG LYS GLN ALA THR TYR GLY ASP ALA GLY LEU SEQRES 6 A 203 THR TYR THR PHE SER GLY LEU THR LEU SER PRO LYS PRO SEQRES 7 A 203 TRP ILE PRO VAL LEU GLU ARG ILE ARG ASP HIS VAL SER SEQRES 8 A 203 GLY VAL THR GLY GLN THR PHE ASN PHE VAL LEU ILE ASN SEQRES 9 A 203 ARG TYR LYS ASP GLY SER ASP HIS ILE GLY GLU HIS ARG SEQRES 10 A 203 ASP ASP CYS ARG GLU LEU ALA PRO GLY SER PRO ILE ALA SEQRES 11 A 203 SER VAL SER PHE GLY ALA SER ARG ASP PHE VAL PHE ARG SEQRES 12 A 203 HIS LYS ASP SER ARG GLY LYS SER PRO SER ARG ARG VAL SEQRES 13 A 203 ALA VAL VAL ARG LEU PRO LEU ALA HIS GLY SER LEU LEU SEQRES 14 A 203 MET MET ASN HIS PRO THR ASN THR HIS TRP TYR HIS SER SEQRES 15 A 203 LEU PRO VAL ARG LYS LYS VAL LEU ALA PRO ARG VAL ASN SEQRES 16 A 203 LEU THR PHE ARG LYS ILE LEU LEU SEQRES 1 B 13 DC DT DG DT DA DT 2YR DA DT DT DG DC DG SEQRES 1 C 13 DT DC DG DC DA DA DT DA DA DT DA DC DA HET 2YR B 7 22 HET AKG A 301 10 HET MN A 302 1 HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM AKG 2-OXOGLUTARIC ACID HETNAM MN MANGANESE (II) ION FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 AKG C5 H6 O5 FORMUL 5 MN MN 2+ FORMUL 6 HOH *91(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 SER A 67 N ILE A 60 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 SER A 186 O LEU A 224 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 2.02 LINK O3' DT B 6 P 2YR B 7 1555 1555 1.60 LINK O3' 2YR B 7 P DA B 8 1555 1555 1.59 LINK NE2 HIS A 171 MN MN A 302 1555 1555 2.25 LINK OD1 ASP A 173 MN MN A 302 1555 1555 2.40 LINK NE2 HIS A 236 MN MN A 302 1555 1555 2.21 LINK O5 AKG A 301 MN MN A 302 1555 1555 2.12 LINK O2 AKG A 301 MN MN A 302 1555 1555 2.31 LINK MN MN A 302 O HOH A 451 1555 1555 2.12 CISPEP 1 HIS A 228 PRO A 229 0 2.96 SITE 1 AC1 13 LEU A 157 ASN A 159 TYR A 161 ILE A 168 SITE 2 AC1 13 HIS A 171 ASP A 173 HIS A 236 ARG A 248 SITE 3 AC1 13 ASN A 250 ARG A 254 MN A 302 HOH A 405 SITE 4 AC1 13 HOH A 451 SITE 1 AC2 5 HIS A 171 ASP A 173 HIS A 236 AKG A 301 SITE 2 AC2 5 HOH A 451 CRYST1 77.591 77.591 227.051 90.00 90.00 120.00 P 65 2 2 12 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 0.012888 0.007441 0.000000 0.00000 SCALE2 0.000000 0.014882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004404 0.00000