HEADER OXIDOREDUCTASE 21-JUL-10 3O1R TITLE IRON-CATALYZED OXIDATION INTERMEDIATES CAPTURED IN A DNA REPAIR TITLE 2 DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINUS 11 AMINO ACID TRUNCATED ALKB (UNP RESIDUES 12 TO COMPND 5 216); COMPND 6 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDK)P*AP*CP*CP*GP*T)-3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: ALKB, AIDD, B2212, JW2200; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: D3-157; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SOLID STATE DNA SYNTHESIZER.; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SOLID STATE DNA SYNTHESIZER. KEYWDS DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,G.JIA,G.HOU,Q.DAI,W.ZHANG,G.ZHENG,X.JIAN,C.-G.YANG,Q.CUI,C.HE REVDAT 5 30-OCT-24 3O1R 1 REMARK REVDAT 4 06-SEP-23 3O1R 1 REMARK SEQADV LINK REVDAT 3 28-MAY-14 3O1R 1 ATOM HET HETATM HETNAM REVDAT 3 2 1 LINK REVDAT 2 19-JUN-13 3O1R 1 JRNL VERSN REVDAT 1 17-NOV-10 3O1R 0 JRNL AUTH C.YI,G.JIA,G.HOU,Q.DAI,W.ZHANG,G.ZHENG,X.JIAN,C.G.YANG, JRNL AUTH 2 Q.CUI,C.HE JRNL TITL IRON-CATALYSED OXIDATION INTERMEDIATES CAPTURED IN A DNA JRNL TITL 2 REPAIR DIOXYGENASE. JRNL REF NATURE V. 468 330 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 21068844 JRNL DOI 10.1038/NATURE09497 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0073 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28207 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1511 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2064 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1580 REMARK 3 NUCLEIC ACID ATOMS : 501 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.44000 REMARK 3 B22 (A**2) : -1.24000 REMARK 3 B33 (A**2) : 2.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.025 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2290 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3221 ; 1.636 ; 2.262 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 6.168 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;36.581 ;22.987 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 261 ;13.724 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.017 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 343 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1607 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1037 ; 0.764 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1671 ; 1.403 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1253 ; 2.180 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1549 ; 3.204 ; 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): -1.8120 1.6740 25.5830 REMARK 3 T TENSOR REMARK 3 T11: -0.0086 T22: -0.0233 REMARK 3 T33: -0.0205 T12: 0.0003 REMARK 3 T13: -0.0021 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 1.0138 L22: 1.3297 REMARK 3 L33: 0.3406 L12: -0.0218 REMARK 3 L13: -0.1708 L23: 0.2811 REMARK 3 S TENSOR REMARK 3 S11: -0.0111 S12: -0.0041 S13: 0.0784 REMARK 3 S21: -0.0675 S22: 0.0161 S23: 0.0230 REMARK 3 S31: 0.0062 S32: 0.0190 S33: -0.0050 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 6 REMARK 3 RESIDUE RANGE : C 9 C 13 REMARK 3 ORIGIN FOR THE GROUP (A): -10.7540 -9.1720 2.1660 REMARK 3 T TENSOR REMARK 3 T11: -0.0288 T22: 0.0610 REMARK 3 T33: -0.0929 T12: 0.0763 REMARK 3 T13: -0.0331 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 8.2301 L22: 5.2618 REMARK 3 L33: 15.0807 L12: -2.3144 REMARK 3 L13: 7.7296 L23: -0.1444 REMARK 3 S TENSOR REMARK 3 S11: 0.2581 S12: 0.7419 S13: -0.1027 REMARK 3 S21: -0.1135 S22: -0.0810 S23: 0.6021 REMARK 3 S31: -0.5343 S32: 0.4807 S33: -0.1771 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 7 B 13 REMARK 3 RESIDUE RANGE : C 1 C 8 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0180 -16.7710 14.2960 REMARK 3 T TENSOR REMARK 3 T11: 0.0109 T22: -0.0019 REMARK 3 T33: 0.0072 T12: 0.0187 REMARK 3 T13: 0.0011 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 2.6058 L22: 1.7677 REMARK 3 L33: 0.6795 L12: -0.9979 REMARK 3 L13: -0.6285 L23: 1.0959 REMARK 3 S TENSOR REMARK 3 S11: 0.0830 S12: 0.1848 S13: -0.2661 REMARK 3 S21: -0.0436 S22: -0.0693 S23: 0.0073 REMARK 3 S31: -0.0755 S32: 0.0209 S33: -0.0137 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3O1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : 21-ID-D 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 : 29820 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.61800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3BIE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8K, 100 MM SODIUM REMARK 280 CHLORIDE, 25 MM 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 37.91500 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: 4170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 11 REMARK 465 GLN A 12 REMARK 465 LYS A 215 REMARK 465 GLU A 216 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 406 O HOH A 499 2.12 REMARK 500 O HOH A 527 O HOH A 537 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 DG B 3 O4' - C1' - N9 ANGL. DEV. = 7.9 DEGREES REMARK 500 DT B 5 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 6 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 3.3 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 ARG A 24 19.01 59.83 REMARK 500 ILE A 201 -68.73 65.14 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 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 100.1 REMARK 620 3 HIS A 187 NE2 94.7 92.0 REMARK 620 4 AKG A 302 O2 94.3 103.3 160.6 REMARK 620 5 AKG A 302 O5 95.4 163.9 82.4 79.6 REMARK 620 6 HOH A 410 O 173.4 84.0 90.4 79.5 81.0 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O1M RELATED DB: PDB REMARK 900 RELATED ID: 3O1O RELATED DB: PDB REMARK 900 RELATED ID: 3O1P RELATED DB: PDB REMARK 900 RELATED ID: 3O1S RELATED DB: PDB REMARK 900 RELATED ID: 3O1T RELATED DB: PDB REMARK 900 RELATED ID: 3O1U RELATED DB: PDB REMARK 900 RELATED ID: 3O1V RELATED DB: PDB DBREF 3O1R A 12 216 UNP P05050 ALKB_ECOLI 12 216 DBREF 3O1R B 2 13 PDB 3O1R 3O1R 2 13 DBREF 3O1R C 1 13 PDB 3O1R 3O1R 1 13 SEQADV 3O1R MET A 11 UNP P05050 EXPRESSION TAG SEQADV 3O1R CYS A 129 UNP P05050 SER 129 ENGINEERED MUTATION SEQRES 1 A 206 MET GLN GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG SEQRES 2 A 206 ARG PHE ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP SEQRES 3 A 206 ILE ASN ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET SEQRES 4 A 206 VAL THR PRO GLY GLY TYR THR MET SER VAL ALA MET THR SEQRES 5 A 206 ASN CYS GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY SEQRES 6 A 206 TYR LEU TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO SEQRES 7 A 206 TRP PRO ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN SEQRES 8 A 206 ARG ALA ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO SEQRES 9 A 206 ASP ALA CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS SEQRES 10 A 206 LEU CYS LEU HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG SEQRES 11 A 206 ALA PRO ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE SEQRES 12 A 206 PHE GLN PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS SEQRES 13 A 206 ARG LEU LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY SEQRES 14 A 206 GLY GLU SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU SEQRES 15 A 206 LYS ALA GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR SEQRES 16 A 206 ASN LEU THR PHE ARG GLN ALA GLY LYS LYS GLU SEQRES 1 B 12 DA DG DG DT DA DA MDK DA 2YR DC DG DT SEQRES 1 C 13 DA DA DC DG DG DT DA DT DT DA DC DC DT HET MDK B 8 20 HET 2YR B 10 22 HET MN A 301 1 HET AKG A 302 10 HET GOL A 303 6 HETNAM MDK 4-AMINO-1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 MDK PENTOFURANOSYL)-3-METHYLPYRIDIN-2(1H)-ONE HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MDK C11 H17 N2 O7 P FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *359(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 ARG A 210 -1 O TYR A 205 N LEU A 148 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 CYS A 64 -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 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 170 N ALA A 152 LINK SG CYS A 129 S 2YR B 10 1555 1555 2.07 LINK O3' DA B 7 P MDK B 8 1555 1555 1.63 LINK O3' MDK B 8 P DA B 9 1555 1555 1.59 LINK O3' DA B 9 P 2YR B 10 1555 1555 1.61 LINK O3' 2YR B 10 P DC B 11 1555 1555 1.61 LINK NE2 HIS A 131 MN MN A 301 1555 1555 2.17 LINK OD1 ASP A 133 MN MN A 301 1555 1555 2.23 LINK NE2 HIS A 187 MN MN A 301 1555 1555 2.14 LINK MN MN A 301 O2 AKG A 302 1555 1555 2.06 LINK MN MN A 301 O5 AKG A 302 1555 1555 2.19 LINK MN MN A 301 O HOH A 410 1555 1555 2.35 SITE 1 AC1 5 HIS A 131 ASP A 133 HIS A 187 AKG A 302 SITE 2 AC1 5 HOH A 410 SITE 1 AC2 16 ASN A 120 TYR A 122 LEU A 128 HIS A 131 SITE 2 AC2 16 ASP A 133 HIS A 187 ILE A 189 ARG A 204 SITE 3 AC2 16 ASN A 206 ARG A 210 MN A 301 HOH A 410 SITE 4 AC2 16 HOH A 446 HOH A 461 HOH A 550 MDK B 8 SITE 1 AC3 5 ASN A 38 THR A 200 TYR A 205 HOH A 630 SITE 2 AC3 5 HOH A 641 CRYST1 41.465 75.830 51.976 90.00 108.24 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 0.024117 0.000000 0.007948 0.00000 SCALE2 0.000000 0.013187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020258 0.00000