HEADER OXIDOREDUCTASE/DNA 31-DEC-07 3BTX TITLE X-RAY STRUCTURE OF HUMAN ABH2 BOUND TO DSDNA THROUGH ACTIVE SITE TITLE 2 CROSS-LINKING 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- KEYWDS 2 LINKING, 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 7 06-NOV-24 3BTX 1 REMARK REVDAT 6 20-OCT-21 3BTX 1 REMARK SEQADV LINK REVDAT 5 21-MAY-14 3BTX 1 COMPND REMARK SEQRES HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 HETATM ATOM REVDAT 4 13-JUL-11 3BTX 1 VERSN REVDAT 3 24-FEB-09 3BTX 1 VERSN REVDAT 2 10-JUN-08 3BTX 1 JRNL REVDAT 1 22-APR-08 3BTX 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 26213 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1423 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1608 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1636 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 192 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) : 43.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.42000 REMARK 3 B12 (A**2) : -0.14000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.452 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2340 ; 0.007 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3285 ; 1.206 ; 2.234 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 220 ; 5.485 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;26.241 ;21.205 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 301 ;12.988 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 356 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1624 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 858 ; 0.171 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1485 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 205 ; 0.121 ; 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): 37 ; 0.156 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.190 ; 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): 1080 ; 0.384 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1705 ; 0.669 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1597 ; 1.004 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1573 ; 1.624 ; 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 258 REMARK 3 ORIGIN FOR THE GROUP (A): 110.5076 -2.4455-194.9771 REMARK 3 T TENSOR REMARK 3 T11: -0.1568 T22: -0.1853 REMARK 3 T33: -0.1434 T12: -0.0166 REMARK 3 T13: 0.0552 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 5.2437 L22: 3.7851 REMARK 3 L33: 1.5170 L12: -2.2613 REMARK 3 L13: 0.4794 L23: -0.7521 REMARK 3 S TENSOR REMARK 3 S11: 0.0972 S12: 0.3139 S13: -0.2067 REMARK 3 S21: -0.5901 S22: 0.0930 S23: -0.0939 REMARK 3 S31: 0.1978 S32: -0.0014 S33: -0.1902 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 259 B 271 REMARK 3 ORIGIN FOR THE GROUP (A): 87.9091 2.4348-195.3908 REMARK 3 T TENSOR REMARK 3 T11: -0.0712 T22: -0.1027 REMARK 3 T33: -0.1193 T12: 0.0405 REMARK 3 T13: 0.0245 T23: 0.1817 REMARK 3 L TENSOR REMARK 3 L11: 4.1413 L22: 1.2854 REMARK 3 L33: 2.0222 L12: 1.4087 REMARK 3 L13: 1.1010 L23: 1.2687 REMARK 3 S TENSOR REMARK 3 S11: -0.1789 S12: -0.2030 S13: -0.1360 REMARK 3 S21: -0.1472 S22: 0.2430 S23: 0.3376 REMARK 3 S31: 0.0658 S32: -0.3868 S33: -0.0641 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 272 C 284 REMARK 3 ORIGIN FOR THE GROUP (A): 90.0645 4.0602-194.8220 REMARK 3 T TENSOR REMARK 3 T11: -0.1328 T22: 0.0006 REMARK 3 T33: -0.1319 T12: -0.0411 REMARK 3 T13: 0.0096 T23: 0.1271 REMARK 3 L TENSOR REMARK 3 L11: 2.7178 L22: 3.2106 REMARK 3 L33: 16.1318 L12: -1.4418 REMARK 3 L13: 3.3653 L23: -5.1379 REMARK 3 S TENSOR REMARK 3 S11: -0.0902 S12: -0.3987 S13: -0.1611 REMARK 3 S21: -0.1325 S22: 0.3980 S23: 0.5003 REMARK 3 S31: -0.2811 S32: -0.4573 S33: -0.3077 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 3BTX 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_1000045951. 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) : 0.9266 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 : 28880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 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 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 153.06000 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 76.53000 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 114.79500 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 38.26500 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 191.32500 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 153.06000 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 76.53000 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 38.26500 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 114.79500 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 191.32500 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: 4020 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 262 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT B 267 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 268 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC C 275 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT C 278 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA C 279 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 280 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 283 O4' - C1' - N1 ANGL. DEV. = 2.2 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 -171.71 176.37 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 173 OD1 REMARK 620 2 ASP A 173 OD2 49.3 REMARK 620 3 HOH A 518 O 69.1 100.1 REMARK 620 4 HOH A 519 O 131.4 108.4 75.9 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 MG A 301 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: 3BTY RELATED DB: PDB REMARK 900 RELATED ID: 3BTZ RELATED DB: PDB REMARK 900 RELATED ID: 3BU0 RELATED DB: PDB REMARK 900 RELATED ID: 3BUC RELATED DB: PDB DBREF 3BTX A 56 258 UNP Q6NS38 ALKB2_HUMAN 56 258 DBREF 3BTX B 259 271 PDB 3BTX 3BTX 259 271 DBREF 3BTX C 272 284 PDB 3BTX 3BTX 272 284 SEQADV 3BTX ALA A 55 UNP Q6NS38 EXPRESSION TAG SEQADV 3BTX SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3BTX SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3BTX CYS A 175 UNP Q6NS38 GLU 175 ENGINEERED MUTATION SEQADV 3BTX SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQRES 1 A 204 ALA SER TRP ARG HIS ILE ARG ALA GLU GLY LEU ASP SER SEQRES 2 A 204 SER TYR THR VAL LEU PHE GLY LYS ALA GLU ALA ASP GLU SEQRES 3 A 204 ILE PHE GLN GLU LEU GLU LYS GLU VAL GLU TYR PHE THR SEQRES 4 A 204 GLY ALA LEU ALA ARG VAL GLN VAL PHE GLY LYS TRP HIS SEQRES 5 A 204 SER VAL PRO ARG LYS GLN ALA THR TYR GLY ASP ALA GLY SEQRES 6 A 204 LEU THR TYR THR PHE SER GLY LEU THR LEU SER PRO LYS SEQRES 7 A 204 PRO TRP ILE PRO VAL LEU GLU ARG ILE ARG ASP HIS VAL SEQRES 8 A 204 SER GLY VAL THR GLY GLN THR PHE ASN PHE VAL LEU ILE SEQRES 9 A 204 ASN ARG TYR LYS ASP GLY SER ASP HIS ILE GLY GLU HIS SEQRES 10 A 204 ARG ASP ASP CYS ARG GLU LEU ALA PRO GLY SER PRO ILE SEQRES 11 A 204 ALA SER VAL SER PHE GLY ALA SER ARG ASP PHE VAL PHE SEQRES 12 A 204 ARG HIS LYS ASP SER ARG GLY LYS SER PRO SER ARG ARG SEQRES 13 A 204 VAL ALA VAL VAL ARG LEU PRO LEU ALA HIS GLY SER LEU SEQRES 14 A 204 LEU MET MET ASN HIS PRO THR ASN THR HIS TRP TYR HIS SEQRES 15 A 204 SER LEU PRO VAL ARG LYS LYS VAL LEU ALA PRO ARG VAL SEQRES 16 A 204 ASN 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 265 22 HET MG A 301 1 HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM MG MAGNESIUM ION FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MG MG 2+ FORMUL 5 HOH *192(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 LEU A 157 O THR A 252 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 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 VAL A 214 N PHE A 197 LINK SG CYS A 175 S 2YR B 265 1555 1555 2.03 LINK O3' DT B 264 P 2YR B 265 1555 1555 1.60 LINK O3' 2YR B 265 P DA B 266 1555 1555 1.59 LINK OD1 ASP A 173 MG MG A 301 1555 1555 2.58 LINK OD2 ASP A 173 MG MG A 301 1555 1555 2.67 LINK MG MG A 301 O HOH A 518 1555 1555 2.40 LINK MG MG A 301 O HOH A 519 1555 1555 2.43 CISPEP 1 HIS A 228 PRO A 229 0 2.21 SITE 1 AC1 5 HIS A 171 ASP A 173 HIS A 236 HOH A 518 SITE 2 AC1 5 HOH A 519 CRYST1 78.140 78.140 229.590 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 0.012798 0.007389 0.000000 0.00000 SCALE2 0.000000 0.014777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004356 0.00000