PDB Short entry for 2XO7 HEADER TRANSFERASE/DNA 10-AUG-10 2XO7 TITLE CRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX TITLE 2 WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 297-876; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3'; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: POLYDESOXYRIBONUCLEOTIDE; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3'; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: POLYDESOXYRIBONUCLEOTIDE; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 STRAIN: DSM 22; SOURCE 5 ATCC: 12980; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX, EPIGENETICS, PYROSEQUENCING EXPDTA X-RAY DIFFRACTION AUTHOR M.MUENZEL,L.LERCHER,M.MUELLER,T.CARELL REVDAT 4 20-DEC-23 2XO7 1 REMARK SEQRES LINK REVDAT 3 21-SEP-11 2XO7 1 JRNL REMARK VERSN REVDAT 2 24-NOV-10 2XO7 1 KEYWDS JRNL REVDAT 1 15-SEP-10 2XO7 0 JRNL AUTH M.MUENZEL,L.LERCHER,M.MUELLER,T.CARELL JRNL TITL CHEMICAL DISCRIMINATION BETWEEN DC AND 5MEDC VIA THEIR JRNL TITL 2 HYDROXYLAMINE ADDUCTS JRNL REF NUCLEIC ACIDS RES. V. 38 E192 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20813757 JRNL DOI 10.1093/NAR/GKQ724 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19570 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1047 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4633 REMARK 3 NUCLEIC ACID ATOMS : 428 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.92000 REMARK 3 B22 (A**2) : -3.45000 REMARK 3 B33 (A**2) : -1.47000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.362 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.254 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.727 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5210 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3470 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7130 ; 1.384 ; 2.082 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8458 ; 0.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 4.878 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;36.473 ;24.115 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 869 ;18.074 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;18.326 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 801 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5431 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 979 ; 0.001 ; 0.020 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): 2898 ; 0.470 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1160 ; 0.089 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4669 ; 0.967 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2312 ; 1.675 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2461 ; 2.917 ; 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 : NULL 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 2XO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1290044980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20704 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 43.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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 1U45 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50-55% (NH4)2SO4 3-3.5% MPD 100MM MES, REMARK 280 PH 5.8 10MG/ML PROTEIN/DNA 1:3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 43.73900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.54550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.81800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.54550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.73900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.81800 REMARK 290 SMTRY3 4 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: 4870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.4 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 GLU A 520 CD OE1 OE2 REMARK 470 GLU A 525 CG CD OE1 OE2 REMARK 470 ASP A 559 CG OD1 OD2 REMARK 470 TYR A 719 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 729 CB CG CD NE CZ NH1 NH2 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 OD1 ASP A 363 OG1 THR A 365 1.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 309 CB GLU A 309 CG 0.125 REMARK 500 DT C 9 O3' DT C 9 C3' -0.040 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 20 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 24 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 25 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT B 25 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 27 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 27 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 DC B 28 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 29 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 11 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC C 13 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC C 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC C 13 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DA C 14 O4' - C1' - N9 ANGL. DEV. = 4.4 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 ASP A 372 73.59 58.32 REMARK 500 ASP A 402 94.43 -161.90 REMARK 500 ALA A 421 39.70 -83.49 REMARK 500 ALA A 436 134.98 -174.99 REMARK 500 LEU A 477 -71.69 -109.32 REMARK 500 LEU A 610 -48.00 -131.13 REMARK 500 ASN A 726 12.84 83.61 REMARK 500 ILE A 727 -148.30 -117.36 REMARK 500 HIS A 768 22.67 83.77 REMARK 500 VAL A 828 66.51 -117.57 REMARK 500 HIS A 829 -49.72 68.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 877 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 878 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 879 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 887 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XO9 RELATED DB: PDB REMARK 900 CYTOSINE- FAPY G BASE PAIR IN THE ACTIVE SITE DNA POLYMERASE I OF REMARK 900 BACILLUS STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2XOH RELATED DB: PDB REMARK 900 GUANIDINE- FAPY A BASE PAIR IN THE ACTIVE SITE DNA POLYMERASE I OF REMARK 900 BACILLUS STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2XOJ RELATED DB: PDB REMARK 900 THYMIDINE- FAPY A BASE PAIR IN THE ACTIVE SITE DNA POLYMERASE I OF REMARK 900 BACILLUS STEAROTHERMOPHILUS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM REMARK 999 IDENTITY. ONLY T550 IS S IN OUR SEQUENCE.THE CRYSTALLISED REMARK 999 SEQUENCE HAS BEEN MAPPED TO GEOBACILLUS SP. Y412MC52 SINCE REMARK 999 THIS IS THE CLOSEST MATCH AVAILABLE (99.8%). AUTHOR HAS PROVIDED A REMARK 999 GENBANK ACCESSION CODE FOR THE SEQUENCE WHICH IS YP_003670385.1 DBREF 2XO7 A 297 876 UNP C3IXT2 C3IXT2_9BACI 297 876 DBREF 2XO7 B 20 29 PDB 2XO7 2XO7 20 29 DBREF 2XO7 C 4 14 PDB 2XO7 2XO7 4 14 SEQADV 2XO7 ARG A 512 UNP C3IXT2 GLY 512 SEE REMARK 999 SEQADV 2XO7 SER A 550 UNP C3IXT2 THR 550 SEE REMARK 999 SEQRES 1 A 580 ALA LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU SEQRES 2 A 580 GLU MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL SEQRES 3 A 580 VAL GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE SEQRES 4 A 580 ALA VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO SEQRES 5 A 580 GLU THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU SEQRES 6 A 580 GLY ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS SEQRES 7 A 580 ARG ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU SEQRES 8 A 580 CYS GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU SEQRES 9 A 580 LEU ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA SEQRES 10 A 580 ALA LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU SEQRES 11 A 580 ALA VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP SEQRES 12 A 580 GLU PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA SEQRES 13 A 580 ALA ILE TRP ALA LEU GLU ARG PRO PHE LEU ASP GLU LEU SEQRES 14 A 580 ARG ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU SEQRES 15 A 580 GLN PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA SEQRES 16 A 580 GLY VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY SEQRES 17 A 580 GLU GLU LEU ALA GLU GLN LEU ARG THR VAL GLU GLN ARG SEQRES 18 A 580 ILE TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER SEQRES 19 A 580 PRO LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN SEQRES 20 A 580 LEU PRO VAL LEU LYS LYS SER LYS THR GLY TYR SER THR SEQRES 21 A 580 SER ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU SEQRES 22 A 580 ILE VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS SEQRES 23 A 580 LEU GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL SEQRES 24 A 580 ARG PRO ASP THR LYS LYS VAL HIS THR ILE PHE ASN GLN SEQRES 25 A 580 ALA LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO SEQRES 26 A 580 ASN LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG SEQRES 27 A 580 LYS ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP SEQRES 28 A 580 LEU ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG SEQRES 29 A 580 VAL LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU SEQRES 30 A 580 ALA PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA SEQRES 31 A 580 MET ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO SEQRES 32 A 580 ASN MET ARG ARG GLN ALA LYS ALA VAL ASN PHE GLY ILE SEQRES 33 A 580 VAL TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU SEQRES 34 A 580 ASN ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG SEQRES 35 A 580 TYR PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU SEQRES 36 A 580 ASN ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR SEQRES 37 A 580 THR LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SEQRES 38 A 580 SER ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET SEQRES 39 A 580 ALA MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE SEQRES 40 A 580 ILE LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS SEQRES 41 A 580 GLU GLU ARG LEU GLN ALA ARG LEU LEU LEU GLN VAL HIS SEQRES 42 A 580 ASP GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU SEQRES 43 A 580 ARG LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA SEQRES 44 A 580 VAL THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR SEQRES 45 A 580 GLY SER THR TRP TYR ASP ALA LYS SEQRES 1 B 10 DG DA DC DC DA DT 47C DC DC DT SEQRES 1 C 11 DA DG DG DA DA DT DG DG DT DC DA MODRES 2XO7 47C B 26 DC HET 47C B 26 23 HET SO4 A 877 5 HET SO4 A 878 5 HET SO4 A 879 5 HET SO4 A 887 5 HETNAM 47C 2'-DEOXY-N-(PROP-2-EN-1-YLOXY)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 47C PHOSPHATE) HETNAM SO4 SULFATE ION FORMUL 2 47C C12 H18 N3 O8 P FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 HOH *7(H2 O) HELIX 1 1 THR A 308 LEU A 312 5 5 HELIX 2 2 ARG A 347 ALA A 353 1 7 HELIX 3 3 ASP A 354 ASP A 363 1 10 HELIX 4 4 ASP A 372 TRP A 382 1 11 HELIX 5 5 LEU A 394 ASP A 402 1 9 HELIX 6 6 PRO A 403 GLY A 406 5 4 HELIX 7 7 ASP A 409 MET A 416 1 8 HELIX 8 8 PRO A 424 GLY A 430 1 7 HELIX 9 9 LYS A 431 ARG A 435 5 5 HELIX 10 10 ASP A 439 ASN A 468 1 30 HELIX 11 11 GLN A 470 LEU A 477 1 8 HELIX 12 12 LEU A 477 GLY A 492 1 16 HELIX 13 13 ASP A 496 GLY A 523 1 28 HELIX 14 14 SER A 530 GLU A 540 1 11 HELIX 15 15 SER A 557 ALA A 565 1 9 HELIX 16 16 PRO A 566 HIS A 568 5 3 HELIX 17 17 GLU A 569 TYR A 587 1 19 HELIX 18 18 ILE A 588 LYS A 593 1 6 HELIX 19 19 LEU A 630 LYS A 635 1 6 HELIX 20 20 ILE A 636 GLN A 638 5 3 HELIX 21 21 GLN A 656 GLU A 667 1 12 HELIX 22 22 ASP A 668 ARG A 677 1 10 HELIX 23 23 ASP A 680 PHE A 690 1 11 HELIX 24 24 SER A 693 VAL A 697 5 5 HELIX 25 25 THR A 698 GLY A 715 1 18 HELIX 26 26 SER A 717 ASN A 726 1 10 HELIX 27 27 SER A 728 PHE A 743 1 16 HELIX 28 28 PHE A 743 GLY A 761 1 19 HELIX 29 29 PRO A 774 SER A 778 5 5 HELIX 30 30 ASN A 780 GLU A 818 1 39 HELIX 31 31 GLU A 840 GLN A 854 1 15 SHEET 1 AA 6 THR A 302 ALA A 304 0 SHEET 2 AA 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 AA 6 GLY A 334 ASN A 339 -1 O ILE A 335 N LEU A 346 SHEET 4 AA 6 LYS A 315 GLU A 321 -1 O ALA A 317 N VAL A 338 SHEET 5 AA 6 LYS A 367 MET A 370 1 O LYS A 367 N ALA A 316 SHEET 6 AA 6 VAL A 390 ASP A 393 1 N SER A 391 O LYS A 368 SHEET 1 AB 3 LYS A 601 VAL A 602 0 SHEET 2 AB 3 VAL A 493 VAL A 495 -1 O VAL A 493 N VAL A 602 SHEET 3 AB 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 AC 2 LYS A 549 SER A 550 0 SHEET 2 AC 2 GLY A 553 TYR A 554 -1 O GLY A 553 N SER A 550 SHEET 1 AD 2 ILE A 605 ASN A 607 0 SHEET 2 AD 2 SER A 617 THR A 619 -1 O SER A 617 N ASN A 607 SHEET 1 AE 4 ARG A 823 GLN A 827 0 SHEET 2 AE 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 AE 4 TRP A 647 TYR A 654 -1 O LEU A 648 N ALA A 836 SHEET 4 AE 4 VAL A 864 GLY A 869 -1 O ASP A 865 N ASP A 653 SHEET 1 AF 2 TYR A 762 THR A 764 0 SHEET 2 AF 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 LINK O3' DT B 25 P 47C B 26 1555 1555 1.59 LINK O3' 47C B 26 P DC B 27 1555 1555 1.59 CISPEP 1 GLU A 620 PRO A 621 0 2.93 SITE 1 AC1 2 ARG A 702 LYS A 706 SITE 1 AC2 3 ALA A 300 ARG A 343 ARG A 677 SITE 1 AC3 3 HIS A 568 ARG A 779 ARG A 819 SITE 1 AC4 2 SER A 655 GLN A 656 CRYST1 87.478 93.636 105.091 90.00 90.00 90.00 P 21 21 21 4 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 0.011431 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010680 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009516 0.00000