HEADER LIGASE 01-MAR-11 3QXJ TITLE CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER TITLE 2 PYLORI COMPLEXED WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DETHIOBIOTIN SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DTB SYNTHETASE, DTBS, DETHIOBIOTIN SYNTHASE; COMPND 5 EC: 6.3.3.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: 26695; SOURCE 6 GENE: BIOD, HP0029, HP_0029; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD(DE3) MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P11 KEYWDS DTBS, DETHIOBIOTIN SYNTHETASE, ADP BINDING, STRUCTURAL GENOMICS, PSI- KEYWDS 2 BIOLOGY, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.M.KLIMECKA,P.J.POREBSKI,M.CHRUSZCZ,K.MURZYN,A.JOACHIMIAK,W.MINOR, AUTHOR 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 13-SEP-23 3QXJ 1 REMARK REVDAT 4 13-APR-22 3QXJ 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 27-MAR-13 3QXJ 1 JRNL REVDAT 2 28-MAR-12 3QXJ 1 JRNL VERSN REVDAT 1 30-MAR-11 3QXJ 0 JRNL AUTH P.J.POREBSKI,M.KLIMECKA,M.CHRUSZCZ,R.A.NICHOLLS,K.MURZYN, JRNL AUTH 2 M.E.CUFF,X.XU,M.CYMBOROWSKI,G.N.MURSHUDOV,A.SAVCHENKO, JRNL AUTH 3 A.EDWARDS,W.MINOR JRNL TITL STRUCTURAL CHARACTERIZATION OF HELICOBACTER PYLORI JRNL TITL 2 DETHIOBIOTIN SYNTHETASE REVEALS DIFFERENCES BETWEEN FAMILY JRNL TITL 3 MEMBERS. JRNL REF FEBS J. V. 279 1093 2012 JRNL REFN ISSN 1742-464X JRNL PMID 22284390 JRNL DOI 10.1111/J.1742-4658.2012.08506.X REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 40040 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2142 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.4050 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1756 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 301 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.38000 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): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.791 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1921 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1277 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2605 ; 1.900 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3155 ; 2.297 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 6.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 84 ;34.814 ;25.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 337 ;11.066 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;21.008 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2105 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 353 ; 0.007 ; 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): 1170 ; 1.077 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 467 ; 0.209 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1898 ; 1.808 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 751 ; 2.815 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 702 ; 4.373 ; 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 -3 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5090 -22.5110 -11.6010 REMARK 3 T TENSOR REMARK 3 T11: 0.0556 T22: 0.0692 REMARK 3 T33: 0.0321 T12: -0.0180 REMARK 3 T13: 0.0025 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 1.0593 L22: 0.4256 REMARK 3 L33: 0.6470 L12: 0.0295 REMARK 3 L13: 0.1988 L23: 0.2096 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: -0.0710 S13: -0.0371 REMARK 3 S21: 0.0502 S22: -0.0130 S23: 0.0346 REMARK 3 S31: 0.0965 S32: -0.0285 S33: 0.0060 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 : A 101 A 175 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2690 -13.2480 -20.9670 REMARK 3 T TENSOR REMARK 3 T11: 0.0581 T22: 0.0672 REMARK 3 T33: 0.0533 T12: -0.0126 REMARK 3 T13: -0.0071 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.5164 L22: 0.2983 REMARK 3 L33: 0.7942 L12: 0.0136 REMARK 3 L13: 0.2354 L23: 0.1393 REMARK 3 S TENSOR REMARK 3 S11: -0.0027 S12: -0.0252 S13: 0.0639 REMARK 3 S21: -0.0085 S22: -0.0031 S23: 0.0255 REMARK 3 S31: -0.0618 S32: -0.0365 S33: 0.0059 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 : A 176 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0950 -18.4370 -30.1560 REMARK 3 T TENSOR REMARK 3 T11: 0.0457 T22: 0.0960 REMARK 3 T33: 0.0889 T12: -0.0050 REMARK 3 T13: 0.0045 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.6949 L22: 1.0530 REMARK 3 L33: 2.3032 L12: -0.1277 REMARK 3 L13: 0.2345 L23: 0.5111 REMARK 3 S TENSOR REMARK 3 S11: 0.0319 S12: 0.0049 S13: 0.0745 REMARK 3 S21: -0.0267 S22: 0.0327 S23: 0.0067 REMARK 3 S31: -0.0009 S32: 0.1404 S33: -0.0645 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 3QXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.9793 REMARK 200 MONOCHROMATOR : SI-111 CHANNEL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42504 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 35.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : 0.40000 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2QMO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350; 150 MM NH4NO3; 100 MM, REMARK 280 BIS-TRIS; SOAKED WITH 10 MM GTP, 10 MM MGCL2, 10 MM 8- REMARK 280 AMINOOCTANOIC ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.07550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.75200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.07550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.75200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 13.45611 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -67.77206 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 324 LIES ON A SPECIAL POSITION. 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 ARG A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 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 ASN A 179 CG OD1 ND2 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 89 58.70 -144.94 REMARK 500 ASN A 179 4.50 84.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GTP A 221 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 224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 ASP A 50 OD2 87.4 REMARK 620 3 GLU A 116 OE2 83.2 88.3 REMARK 620 4 GTP A 221 O3G 175.9 95.9 94.4 REMARK 620 5 GTP A 221 O1B 88.9 171.8 98.6 88.2 REMARK 620 6 HOH A 374 O 88.8 87.3 171.0 93.8 85.2 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 GTP A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 223 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 229 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 231 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 232 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC5858 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2QMO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI REMARK 900 RELATED ID: 3MLE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COCRYSTALLIZED WITH ATP REMARK 900 RELATED ID: 3QXC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH ATP REMARK 900 RELATED ID: 3QXH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH ADP AND 8-AMINOCAPRYLIC ACID REMARK 900 RELATED ID: 3QXS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH ANP REMARK 900 RELATED ID: 3QXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH GDP AND 8-AMINOCAPRYLIC ACID REMARK 900 RELATED ID: 3QY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH GDP DBREF 3QXJ A 1 218 UNP O24872 BIOD_HELPY 1 218 SEQADV 3QXJ MET A -21 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLY A -20 UNP O24872 EXPRESSION TAG SEQADV 3QXJ SER A -19 UNP O24872 EXPRESSION TAG SEQADV 3QXJ SER A -18 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -17 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -16 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -15 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -14 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -13 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A -12 UNP O24872 EXPRESSION TAG SEQADV 3QXJ SER A -11 UNP O24872 EXPRESSION TAG SEQADV 3QXJ SER A -10 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLY A -9 UNP O24872 EXPRESSION TAG SEQADV 3QXJ ARG A -8 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLU A -7 UNP O24872 EXPRESSION TAG SEQADV 3QXJ ASN A -6 UNP O24872 EXPRESSION TAG SEQADV 3QXJ LEU A -5 UNP O24872 EXPRESSION TAG SEQADV 3QXJ TYR A -4 UNP O24872 EXPRESSION TAG SEQADV 3QXJ PHE A -3 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLN A -2 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLY A -1 UNP O24872 EXPRESSION TAG SEQADV 3QXJ HIS A 0 UNP O24872 EXPRESSION TAG SEQADV 3QXJ GLY A 219 UNP O24872 EXPRESSION TAG SEQADV 3QXJ SER A 220 UNP O24872 EXPRESSION TAG SEQRES 1 A 242 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 242 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET LEU PHE ILE SEQRES 3 A 242 SER ALA THR ASN THR ASN ALA GLY LYS THR THR CYS ALA SEQRES 4 A 242 ARG LEU LEU ALA GLN TYR CYS ASN ALA CYS GLY VAL LYS SEQRES 5 A 242 THR ILE LEU LEU LYS PRO ILE GLU THR GLY VAL ASN ASP SEQRES 6 A 242 ALA ILE ASN HIS SER SER ASP ALA HIS LEU PHE LEU GLN SEQRES 7 A 242 ASP ASN ARG LEU LEU ASP ARG SER LEU THR LEU LYS ASP SEQRES 8 A 242 ILE SER PHE TYR ARG TYR HIS LYS VAL SER ALA PRO LEU SEQRES 9 A 242 ILE ALA GLN GLN GLU GLU ASP PRO ASN ALA PRO ILE ASP SEQRES 10 A 242 THR ASP ASN LEU THR GLN ARG LEU HIS ASN PHE THR LYS SEQRES 11 A 242 THR TYR ASP LEU VAL ILE VAL GLU GLY ALA GLY GLY LEU SEQRES 12 A 242 CYS VAL PRO ILE THR LEU GLU GLU ASN MET LEU ASP PHE SEQRES 13 A 242 ALA LEU LYS LEU LYS ALA LYS MET LEU LEU ILE SER HIS SEQRES 14 A 242 ASP ASN LEU GLY LEU ILE ASN ASP CYS LEU LEU ASN ASP SEQRES 15 A 242 PHE LEU LEU LYS SER HIS GLN LEU ASP TYR LYS ILE ALA SEQRES 16 A 242 ILE ASN LEU LYS GLY ASN ASN THR ALA PHE HIS SER ILE SEQRES 17 A 242 SER LEU PRO TYR ILE GLU LEU PHE ASN THR ARG SER ASN SEQRES 18 A 242 ASN PRO ILE VAL ILE PHE GLN GLN SER LEU LYS VAL LEU SEQRES 19 A 242 MET SER PHE ALA LEU LYS GLY SER HET GTP A 221 22 HET EDO A 222 4 HET EDO A 223 4 HET MG A 224 1 HET EDO A 225 4 HET EDO A 226 4 HET EDO A 227 4 HET NO3 A 228 4 HET EDO A 229 4 HET EDO A 230 4 HET EDO A 231 4 HET EDO A 232 4 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM NO3 NITRATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 EDO 9(C2 H6 O2) FORMUL 5 MG MG 2+ FORMUL 9 NO3 N O3 1- FORMUL 14 HOH *301(H2 O) HELIX 1 1 GLY A 12 CYS A 27 1 16 HELIX 2 2 SER A 49 ARG A 59 1 11 HELIX 3 3 THR A 66 SER A 71 1 6 HELIX 4 4 ALA A 80 ASP A 89 1 10 HELIX 5 5 ASP A 95 PHE A 106 1 12 HELIX 6 6 THR A 107 THR A 109 5 3 HELIX 7 7 ASN A 130 LYS A 139 1 10 HELIX 8 8 GLY A 151 SER A 165 1 15 HELIX 9 9 THR A 181 SER A 187 1 7 HELIX 10 10 SER A 187 SER A 198 1 12 HELIX 11 11 SER A 208 LYS A 218 1 11 SHEET 1 A 6 THR A 31 LEU A 34 0 SHEET 2 A 6 LEU A 112 GLU A 116 1 O ILE A 114 N ILE A 32 SHEET 3 A 6 HIS A 0 ALA A 6 1 N ILE A 4 O VAL A 115 SHEET 4 A 6 LYS A 141 SER A 146 1 O LYS A 141 N PHE A 3 SHEET 5 A 6 TYR A 170 ILE A 174 1 O LYS A 171 N LEU A 144 SHEET 6 A 6 VAL A 203 ILE A 204 1 O VAL A 203 N ILE A 174 SHEET 1 B 2 ILE A 37 GLU A 38 0 SHEET 2 B 2 TYR A 73 ARG A 74 1 O TYR A 73 N GLU A 38 LINK OG1 THR A 14 MG MG A 224 1555 1555 2.11 LINK OD2 ASP A 50 MG MG A 224 1555 1555 2.09 LINK OE2 GLU A 116 MG MG A 224 1555 1555 2.15 LINK O3G GTP A 221 MG MG A 224 1555 1555 1.96 LINK O1B GTP A 221 MG MG A 224 1555 1555 2.12 LINK MG MG A 224 O HOH A 374 1555 1555 2.17 SITE 1 AC1 20 THR A 9 ASN A 10 ALA A 11 GLY A 12 SITE 2 AC1 20 LYS A 13 THR A 14 THR A 15 LYS A 35 SITE 3 AC1 20 ASP A 50 GLU A 116 GLN A 167 MG A 224 SITE 4 AC1 20 EDO A 232 HOH A 279 HOH A 283 HOH A 284 SITE 5 AC1 20 HOH A 374 HOH A 468 HOH A 492 HOH A 520 SITE 1 AC2 6 ASN A 42 ASP A 43 ARG A 74 HIS A 76 SITE 2 AC2 6 HOH A 364 HOH A 451 SITE 1 AC3 4 ASN A 130 ASP A 133 HIS A 166 HOH A 523 SITE 1 AC4 5 THR A 14 ASP A 50 GLU A 116 GTP A 221 SITE 2 AC4 5 HOH A 374 SITE 1 AC5 5 ASN A 25 GLY A 28 LYS A 30 LEU A 61 SITE 2 AC5 5 HOH A 310 SITE 1 AC6 5 HIS A 0 MET A 1 LYS A 139 LYS A 141 SITE 2 AC6 5 SER A 220 SITE 1 AC7 7 LYS A 171 THR A 181 SER A 185 VAL A 211 SITE 2 AC7 7 HOH A 369 HOH A 413 HOH A 512 SITE 1 AC8 10 SER A 5 ALA A 6 LYS A 13 GLY A 117 SITE 2 AC8 10 ALA A 118 GLY A 119 GLY A 120 LEU A 121 SITE 3 AC8 10 MET A 131 HOH A 391 SITE 1 AC9 5 LEU A 168 ASP A 169 TYR A 170 ASN A 200 SITE 2 AC9 5 HOH A 493 SITE 1 BC1 6 GLU A 87 GLU A 88 LEU A 217 HOH A 448 SITE 2 BC1 6 HOH A 481 HOH A 484 SITE 1 BC2 2 ASN A 8 ASN A 149 SITE 1 BC3 7 LYS A 35 GLU A 38 THR A 39 ALA A 118 SITE 2 BC3 7 GTP A 221 HOH A 492 HOH A 520 CRYST1 82.151 37.504 69.095 90.00 101.23 90.00 C 1 2 1 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 0.012173 0.000000 0.002418 0.00000 SCALE2 0.000000 0.026664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014756 0.00000