HEADER OXIDOREDUCTASE/DNA 30-NOV-07 3BIE TITLE X-RAY STRUCTURE OF E COLI ALKB BOUND TO DSDNA CONTAINING 1MEA/T WITH TITLE 2 MN AND 2KG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7) COMPND 11 P*DAP*DCP*DCP*DGP*DT)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3'); COMPND 17 CHAIN: C; COMPND 18 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 DIOXYGENASE, PROTEIN DNA INTERACTION, CROSS-LINKING, ALKYLATION KEYWDS 2 REPAIR, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,C.-G.YANG REVDAT 7 16-OCT-24 3BIE 1 REMARK REVDAT 6 20-OCT-21 3BIE 1 REMARK DBREF SEQADV LINK REVDAT 5 28-MAY-14 3BIE 1 ATOM HET HETATM HETNAM REVDAT 5 2 1 LINK REVDAT 4 13-JUL-11 3BIE 1 VERSN REVDAT 3 24-FEB-09 3BIE 1 VERSN REVDAT 2 22-JUL-08 3BIE 1 JRNL REMARK REVDAT 1 22-APR-08 3BIE 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. 1.68 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 30668 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1624 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) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1581 REMARK 3 NUCLEIC ACID ATOMS : 505 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 259 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) : 24.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.39000 REMARK 3 B22 (A**2) : -1.19000 REMARK 3 B33 (A**2) : 2.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 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): 2201 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3091 ; 1.099 ; 2.253 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 5.562 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;35.140 ;23.026 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 250 ;12.284 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;12.316 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 331 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1545 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 872 ; 0.174 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1393 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 242 ; 0.089 ; 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 ; 0.080 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.055 ; 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): 1045 ; 0.350 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1622 ; 0.538 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1495 ; 0.648 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1469 ; 1.033 ; 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 13 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): -2.0043 1.5188 25.6307 REMARK 3 T TENSOR REMARK 3 T11: -0.1109 T22: -0.1150 REMARK 3 T33: -0.1392 T12: 0.0019 REMARK 3 T13: -0.0089 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 2.0197 L22: 2.1063 REMARK 3 L33: 0.3852 L12: -0.0342 REMARK 3 L13: -0.3380 L23: 0.4260 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.0643 S13: 0.1004 REMARK 3 S21: -0.1331 S22: 0.0103 S23: 0.0385 REMARK 3 S31: -0.0168 S32: 0.0119 S33: 0.0010 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 2 B 13 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5450 -12.7015 10.2799 REMARK 3 T TENSOR REMARK 3 T11: -0.0189 T22: -0.0390 REMARK 3 T33: -0.0615 T12: 0.0219 REMARK 3 T13: -0.0153 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 3.3849 L22: 2.4433 REMARK 3 L33: 1.5227 L12: -0.5334 REMARK 3 L13: -1.5541 L23: 1.6266 REMARK 3 S TENSOR REMARK 3 S11: 0.1579 S12: 0.5281 S13: 0.1060 REMARK 3 S21: -0.5202 S22: -0.0740 S23: -0.0467 REMARK 3 S31: -0.2802 S32: -0.2032 S33: -0.0839 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): -0.4079 -15.0631 8.4585 REMARK 3 T TENSOR REMARK 3 T11: 0.0275 T22: 0.0153 REMARK 3 T33: -0.0433 T12: 0.0442 REMARK 3 T13: -0.0006 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 8.2589 L22: 3.0511 REMARK 3 L33: 5.7867 L12: -1.5907 REMARK 3 L13: 3.6383 L23: -0.5958 REMARK 3 S TENSOR REMARK 3 S11: 0.0947 S12: 0.5927 S13: -0.2932 REMARK 3 S21: -0.3085 S22: 0.0538 S23: 0.2497 REMARK 3 S31: -0.1662 S32: -0.3181 S33: -0.1484 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 3BIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045559. 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 : 34683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 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 (%) : 88.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.870 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 (%): 52.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24W/V% PEG 8000, 100MM SODIUM REMARK 280 CHLORIDE, 50MM MAGNESIUM CHLORIDE, 0.1M CACODYLATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, 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 37.91100 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: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.5 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT C 8 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 8 C7 C6 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 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 11 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 12 O4' - C1' - N1 ANGL. DEV. = 2.3 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 -71.58 67.76 REMARK 500 ASP A 202 16.25 -140.01 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 97.5 REMARK 620 3 HIS A 187 NE2 93.1 90.9 REMARK 620 4 AKG A 502 O2 96.2 105.0 160.3 REMARK 620 5 AKG A 502 O5 94.0 168.2 90.9 71.2 REMARK 620 6 HOH A 627 O 175.6 86.5 85.1 84.4 82.0 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: 2IUW RELATED DB: PDB REMARK 900 HOMOLOG REMARK 900 RELATED ID: 2QXQ RELATED DB: PDB REMARK 900 HOMOLOG DBREF 3BIE A 13 214 UNP P05050 ALKB_ECOLI 1 202 DBREF 3BIE B 2 13 PDB 3BIE 3BIE 2 13 DBREF 3BIE C 1 13 PDB 3BIE 3BIE 1 13 SEQADV 3BIE CYS A 129 UNP P05050 SER 117 ENGINEERED MUTATION SEQRES 1 A 202 GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG ARG PHE SEQRES 2 A 202 ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP ILE ASN SEQRES 3 A 202 ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET VAL THR SEQRES 4 A 202 PRO GLY GLY TYR THR MET SER VAL ALA MET THR ASN CYS SEQRES 5 A 202 GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY TYR LEU SEQRES 6 A 202 TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO TRP PRO SEQRES 7 A 202 ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN ARG ALA SEQRES 8 A 202 ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO ASP ALA SEQRES 9 A 202 CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS LEU CYS SEQRES 10 A 202 LEU HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG ALA PRO SEQRES 11 A 202 ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE PHE GLN SEQRES 12 A 202 PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS ARG LEU SEQRES 13 A 202 LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY GLY GLU SEQRES 14 A 202 SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU LYS ALA SEQRES 15 A 202 GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR ASN LEU SEQRES 16 A 202 THR PHE ARG GLN ALA GLY LYS SEQRES 1 B 12 DA DG DG DT DA DA MA7 DA 2YR DC DG DT SEQRES 1 C 13 DA DA DC DG DG DT DT DT DT DA DC DC DT MODRES 3BIE MA7 B 8 DA 1N-METHYLADENOSINE-5'-MONOPHOSPHATE HET MA7 B 8 22 HET 2YR B 10 22 HET MN A 501 1 HET AKG A 502 10 HETNAM MA7 1N-METHYLADENOSINE-5'-MONOPHOSPHATE 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 MA7 C11 H17 N5 O6 P 1+ FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 HOH *259(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 THR A 62 O ILE A 119 SHEET 1 B 2 GLY A 68 HIS A 72 0 SHEET 2 B 2 GLY A 75 SER A 79 -1 O GLY A 75 N HIS A 72 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 170 N ALA A 152 LINK SG CYS A 129 S 2YR B 10 1555 1555 2.04 LINK O3' DA B 7 P MA7 B 8 1555 1555 1.60 LINK O3' MA7 B 8 P DA B 9 1555 1555 1.60 LINK O3' DA B 9 P 2YR B 10 1555 1555 1.60 LINK O3' 2YR B 10 P DC B 11 1555 1555 1.60 LINK NE2 HIS A 131 MN MN A 501 1555 1555 2.18 LINK OD1 ASP A 133 MN MN A 501 1555 1555 2.18 LINK NE2 HIS A 187 MN MN A 501 1555 1555 2.17 LINK MN MN A 501 O2 AKG A 502 1555 1555 2.14 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.42 LINK MN MN A 501 O HOH A 627 1555 1555 2.41 SITE 1 AC1 5 HIS A 131 ASP A 133 HIS A 187 AKG A 502 SITE 2 AC1 5 HOH A 627 SITE 1 AC2 16 LEU A 118 ASN A 120 TYR A 122 LEU A 128 SITE 2 AC2 16 HIS A 131 ASP A 133 HIS A 187 ILE A 189 SITE 3 AC2 16 ARG A 204 ASN A 206 THR A 208 ARG A 210 SITE 4 AC2 16 MN A 501 HOH A 624 HOH A 627 MA7 B 8 CRYST1 41.413 75.822 52.228 90.00 108.53 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 0.024147 0.000000 0.008094 0.00000 SCALE2 0.000000 0.013189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020194 0.00000