HEADER DNA REPAIR,OXIDOREDUCTASE/DNA 09-DEC-07 3BKZ TITLE X-RAY STRUCTURE OF E COLI ALKB CROSSLINKED TO DSDNA IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'- COMPND 10 D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: ALKB, AIDD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS ALKYLATION REPAIR, PROTEIN DNA INTERACTION, CROSS-LINKING, KEYWDS 2 DIOXYGENASE, DNA REPAIR, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,C.-G.YANG,C.HE REVDAT 7 30-OCT-24 3BKZ 1 REMARK REVDAT 6 20-OCT-21 3BKZ 1 REMARK SEQADV LINK REVDAT 5 28-MAY-14 3BKZ 1 ATOM HET HETATM HETNAM REVDAT 5 2 1 LINK REVDAT 4 13-JUL-11 3BKZ 1 VERSN REVDAT 3 24-FEB-09 3BKZ 1 VERSN REVDAT 2 22-JUL-08 3BKZ 1 JRNL REVDAT 1 22-APR-08 3BKZ 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. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31663 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1663 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2264 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1570 REMARK 3 NUCLEIC ACID ATOMS : 529 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 292 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) : 22.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 1.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.664 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2556 ; 0.005 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3641 ; 1.040 ; 2.358 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 206 ; 5.764 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;34.848 ;22.838 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 253 ;11.434 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;11.354 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1712 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 952 ; 0.172 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1589 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 259 ; 0.094 ; 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): 40 ; 0.099 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.063 ; 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): 1052 ; 0.365 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1649 ; 0.530 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1971 ; 0.618 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1992 ; 0.984 ; 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 14 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2693 -1.7559 -21.3648 REMARK 3 T TENSOR REMARK 3 T11: -0.1271 T22: -0.1375 REMARK 3 T33: -0.1617 T12: 0.0064 REMARK 3 T13: -0.0067 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 2.3078 L22: 1.7020 REMARK 3 L33: 0.5352 L12: -0.2984 REMARK 3 L13: -0.3959 L23: 0.1665 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.0812 S13: 0.0567 REMARK 3 S21: -0.0678 S22: -0.0174 S23: 0.0276 REMARK 3 S31: 0.0328 S32: -0.0164 S33: -0.0113 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): -9.6532 -17.5092 -38.6714 REMARK 3 T TENSOR REMARK 3 T11: 0.0116 T22: 0.0022 REMARK 3 T33: -0.0428 T12: 0.0739 REMARK 3 T13: -0.0638 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 2.0943 L22: 0.0158 REMARK 3 L33: 0.3285 L12: 0.1432 REMARK 3 L13: -0.8266 L23: -0.0529 REMARK 3 S TENSOR REMARK 3 S11: 0.1789 S12: 0.5664 S13: -0.1057 REMARK 3 S21: -0.2336 S22: -0.1289 S23: 0.1034 REMARK 3 S31: -0.1182 S32: -0.0441 S33: -0.0500 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): -6.5317 -19.9564 -39.0628 REMARK 3 T TENSOR REMARK 3 T11: -0.0065 T22: 0.0140 REMARK 3 T33: -0.0396 T12: 0.0480 REMARK 3 T13: -0.0003 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 9.2404 L22: 2.7612 REMARK 3 L33: 4.7752 L12: 0.2833 REMARK 3 L13: 4.8320 L23: -0.0471 REMARK 3 S TENSOR REMARK 3 S11: -0.2511 S12: 0.6292 S13: -0.0134 REMARK 3 S21: -0.2119 S22: 0.2313 S23: 0.1444 REMARK 3 S31: -0.2080 S32: 0.0052 S33: 0.0199 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 3BKZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045649. 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 : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36607 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 (%): 47.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 5000, 0.1M SODIUM CHLORIDE, 25 REMARK 280 MM MAGNESIUM CHLORIDE, 0.1M CACODYLATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 37.75350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 3480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.8 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 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 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 2.0 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 ILE A 201 -73.22 68.54 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 98.2 REMARK 620 3 HIS A 187 NE2 91.7 90.5 REMARK 620 4 AKG A 502 O2 92.1 108.3 160.0 REMARK 620 5 AKG A 502 O5 96.9 164.9 88.9 71.2 REMARK 620 6 HOH A 625 O 173.5 86.9 92.4 82.4 78.0 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FD8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 2QXQ RELATED DB: PDB REMARK 900 HUMAN HOMOLOG DBREF 3BKZ A 14 214 UNP P05050 ALKB_ECOLI 14 214 DBREF 3BKZ B 1 13 PDB 3BKZ 3BKZ 1 13 DBREF 3BKZ C 1 13 PDB 3BKZ 3BKZ 1 13 SEQADV 3BKZ CYS A 135 UNP P05050 ASP 135 ENGINEERED MUTATION SEQRES 1 A 201 PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG ARG PHE ALA SEQRES 2 A 201 PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP ILE ASN ASP SEQRES 3 A 201 VAL ALA SER GLN SER PRO PHE ARG GLN MET VAL THR PRO SEQRES 4 A 201 GLY GLY TYR THR MET SER VAL ALA MET THR ASN CYS GLY SEQRES 5 A 201 HIS LEU GLY TRP THR THR HIS ARG GLN GLY TYR LEU TYR SEQRES 6 A 201 SER PRO ILE ASP PRO GLN THR ASN LYS PRO TRP PRO ALA SEQRES 7 A 201 MET PRO GLN SER PHE HIS ASN LEU CYS GLN ARG ALA ALA SEQRES 8 A 201 THR ALA ALA GLY TYR PRO ASP PHE GLN PRO ASP ALA CYS SEQRES 9 A 201 LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS LEU SER LEU SEQRES 10 A 201 HIS GLN ASP LYS CYS GLU PRO ASP LEU ARG ALA PRO ILE SEQRES 11 A 201 VAL SER VAL SER LEU GLY LEU PRO ALA ILE PHE GLN PHE SEQRES 12 A 201 GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS ARG LEU LEU SEQRES 13 A 201 LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY GLY GLU SER SEQRES 14 A 201 ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU LYS ALA GLY SEQRES 15 A 201 PHE HIS PRO LEU THR ILE ASP CYS ARG TYR ASN LEU THR SEQRES 16 A 201 PHE ARG GLN ALA GLY LYS SEQRES 1 B 13 DT DA DG DG DT DA DA 2YR DA DT DC DG DT SEQRES 1 C 13 DA DA DC DG DA DT DA DT DT DA DC DC DT HET 2YR B 8 22 HET MN A 501 1 HET AKG A 502 10 HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 HOH *292(H2 O) HELIX 1 1 ALA A 29 SER A 44 1 16 HELIX 2 2 PRO A 93 ALA A 107 1 15 HELIX 3 3 GLY A 179 ARG A 183 5 5 SHEET 1 A 6 VAL A 20 LEU A 22 0 SHEET 2 A 6 VAL A 175 TRP A 178 -1 O VAL A 175 N LEU A 22 SHEET 3 A 6 ILE A 143 GLY A 149 -1 N SER A 145 O VAL A 176 SHEET 4 A 6 ARG A 204 PHE A 209 -1 O PHE A 209 N VAL A 144 SHEET 5 A 6 ALA A 116 TYR A 122 -1 N TYR A 122 O ARG A 204 SHEET 6 A 6 ALA A 60 GLY A 65 -1 N ALA A 60 O ARG A 121 SHEET 1 B 2 GLY A 68 THR A 71 0 SHEET 2 B 2 TYR A 76 SER A 79 -1 O LEU A 77 N THR A 70 SHEET 1 C 4 LEU A 128 HIS A 131 0 SHEET 2 C 4 HIS A 187 ILE A 189 -1 O ILE A 189 N LEU A 128 SHEET 3 C 4 ALA A 152 PHE A 156 -1 N GLN A 155 O GLY A 188 SHEET 4 C 4 LYS A 166 LEU A 170 -1 O LEU A 168 N PHE A 154 LINK SG CYS A 135 S 2YR B 8 1555 1555 2.03 LINK O3'A DA B 7 P 2YR B 8 1555 1555 1.60 LINK O3'B DA B 7 P 2YR B 8 1555 1555 1.59 LINK O3' 2YR B 8 P DA B 9 1555 1555 1.60 LINK NE2 HIS A 131 MN MN A 501 1555 1555 2.16 LINK OD1 ASP A 133 MN MN A 501 1555 1555 2.22 LINK NE2 HIS A 187 MN MN A 501 1555 1555 2.17 LINK MN MN A 501 O2 AKG A 502 1555 1555 2.30 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.32 LINK MN MN A 501 O HOH A 625 1555 1555 2.30 SITE 1 AC1 5 HIS A 131 ASP A 133 HIS A 187 AKG A 502 SITE 2 AC1 5 HOH A 625 SITE 1 AC2 15 LEU A 118 ASN A 120 TYR A 122 LEU A 128 SITE 2 AC2 15 HIS A 131 ASP A 133 HIS A 187 ILE A 189 SITE 3 AC2 15 ARG A 204 ASN A 206 ARG A 210 MN A 501 SITE 4 AC2 15 HOH A 610 HOH A 625 HOH B 103 CRYST1 41.397 75.507 46.788 90.00 105.45 90.00 P 1 21 1 2 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 0.024156 0.000000 0.006676 0.00000 SCALE2 0.000000 0.013244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022174 0.00000