HEADER LIGASE 01-MAR-11 3QXH TITLE CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER TITLE 2 PYLORI COMPLEXED WITH ADP AND 8-AMINOCAPRYLIC ACID 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, ATP BINDING, STRUCTURAL GENOMICS, PSI- KEYWDS 2 BIOLOGY, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR P.J.POREBSKI,M.M.KLIMECKA,M.CHRUSZCZ,K.MURZYN,C.MINOR,A.JOACHIMIAK, AUTHOR 2 W.MINOR,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 13-SEP-23 3QXH 1 REMARK REVDAT 4 13-APR-22 3QXH 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 27-MAR-13 3QXH 1 JRNL REVDAT 2 28-MAR-12 3QXH 1 JRNL VERSN REVDAT 1 30-MAR-11 3QXH 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. 1.36 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 41354 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) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2190 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) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2583 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.1950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1751 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 353 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.15000 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): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.061 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1968 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1305 ; 0.020 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2682 ; 1.707 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3230 ; 2.307 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 253 ; 6.053 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;35.270 ;25.506 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;11.717 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;16.579 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2185 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 369 ; 0.005 ; 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): 1188 ; 1.801 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 474 ; 2.142 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1936 ; 2.584 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 780 ; 3.912 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 738 ; 5.465 ; 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): 1910 ; 2.096 ; 3.000 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 : 1.20 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 3QXH 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_1000064226. 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) : 100.0 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 : 43544 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : 0.02600 REMARK 200 FOR THE DATA SET : 47.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.07000 REMARK 200 R SYM FOR SHELL (I) : 0.07000 REMARK 200 FOR SHELL : 13.20 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 (%): 36.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350; 150 MM NH4NO3; 100 MM BIS REMARK 280 -TRIS; SOAKED WITH 10 MM ATP, 10 MM MGCL2, 10 MM 8-AMINOOCTANOIC REMARK 280 ACID; IN SITU PROTEOLYSIS - CHYMOTRYPSIN, PH 5.5, VAPOR REMARK 280 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 40.76300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.98350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.76300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.98350 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: 7110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 13.30346 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -67.49645 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 359 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 374 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 GLN A 101 CD OE1 NE2 REMARK 470 ASN A 179 CG OD1 ND2 REMARK 470 LYS A 210 CE NZ 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 129 CD GLU A 129 OE1 -0.080 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 SER A 5 -168.85 -116.43 REMARK 500 ASN A 179 1.87 86.38 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 MG A 223 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 ASP A 50 OD2 80.5 REMARK 620 3 GLU A 116 OE2 84.1 89.6 REMARK 620 4 ADP A 222 O1B 89.8 164.4 101.7 REMARK 620 5 PO4 A 225 O1 170.0 95.5 86.7 95.9 REMARK 620 6 HOH A 337 O 94.1 85.4 175.0 83.0 94.7 REMARK 620 N 1 2 3 4 5 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 ADP A 222 O2B REMARK 620 2 PO4 A 225 O3 100.9 REMARK 620 3 HOH A 307 O 170.6 85.6 REMARK 620 4 HOH A 337 O 86.5 107.4 85.1 REMARK 620 5 HOH A 539 O 92.6 84.0 94.8 168.6 REMARK 620 6 HOH A 540 O 92.5 162.1 82.6 85.1 83.6 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 8AC A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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 PO4 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 EDO 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 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: 3QXJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH GTP 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 3QXH A 1 218 UNP O24872 BIOD_HELPY 1 218 SEQADV 3QXH MET A -21 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLY A -20 UNP O24872 EXPRESSION TAG SEQADV 3QXH SER A -19 UNP O24872 EXPRESSION TAG SEQADV 3QXH SER A -18 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -17 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -16 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -15 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -14 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -13 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A -12 UNP O24872 EXPRESSION TAG SEQADV 3QXH SER A -11 UNP O24872 EXPRESSION TAG SEQADV 3QXH SER A -10 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLY A -9 UNP O24872 EXPRESSION TAG SEQADV 3QXH ARG A -8 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLU A -7 UNP O24872 EXPRESSION TAG SEQADV 3QXH ASN A -6 UNP O24872 EXPRESSION TAG SEQADV 3QXH LEU A -5 UNP O24872 EXPRESSION TAG SEQADV 3QXH TYR A -4 UNP O24872 EXPRESSION TAG SEQADV 3QXH PHE A -3 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLN A -2 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLY A -1 UNP O24872 EXPRESSION TAG SEQADV 3QXH HIS A 0 UNP O24872 EXPRESSION TAG SEQADV 3QXH GLY A 219 UNP O24872 EXPRESSION TAG SEQADV 3QXH 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 8AC A 221 11 HET ADP A 222 27 HET MG A 223 1 HET MG A 224 1 HET PO4 A 225 5 HET EDO A 226 4 HET EDO A 227 4 HET EDO A 228 4 HET EDO A 229 4 HET EDO A 230 4 HETNAM 8AC 8-AMINOOCTANOIC ACID HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN 8AC 8-AMINOCAPRYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8AC C8 H17 N O2 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 PO4 O4 P 3- FORMUL 7 EDO 5(C2 H6 O2) FORMUL 12 HOH *353(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 223 1555 1555 2.15 LINK OD2 ASP A 50 MG MG A 223 1555 1555 2.09 LINK OE2 GLU A 116 MG MG A 223 1555 1555 2.06 LINK O1B ADP A 222 MG MG A 223 1555 1555 2.03 LINK O2B ADP A 222 MG MG A 224 1555 1555 2.07 LINK MG MG A 223 O1 PO4 A 225 1555 1555 2.02 LINK MG MG A 223 O HOH A 337 1555 1555 2.18 LINK MG MG A 224 O3 PO4 A 225 1555 1555 1.99 LINK MG MG A 224 O HOH A 307 1555 1555 2.18 LINK MG MG A 224 O HOH A 337 1555 1555 2.20 LINK MG MG A 224 O HOH A 539 1555 1555 2.19 LINK MG MG A 224 O HOH A 540 1555 1555 2.17 SITE 1 AC1 13 THR A 9 THR A 39 SER A 79 VAL A 123 SITE 2 AC1 13 GLY A 151 LEU A 152 ILE A 153 ASN A 154 SITE 3 AC1 13 PO4 A 225 HOH A 308 HOH A 356 HOH A 493 SITE 4 AC1 13 HOH A 556 SITE 1 AC2 23 ASN A 10 ALA A 11 GLY A 12 LYS A 13 SITE 2 AC2 23 THR A 14 THR A 15 GLU A 116 GLN A 167 SITE 3 AC2 23 ASN A 175 LYS A 177 MG A 223 MG A 224 SITE 4 AC2 23 PO4 A 225 HOH A 335 HOH A 337 HOH A 340 SITE 5 AC2 23 HOH A 392 HOH A 503 HOH A 520 HOH A 539 SITE 6 AC2 23 HOH A 540 HOH A 558 HOH A 563 SITE 1 AC3 8 THR A 14 LYS A 35 ASP A 50 GLU A 116 SITE 2 AC3 8 ADP A 222 MG A 224 PO4 A 225 HOH A 337 SITE 1 AC4 7 ADP A 222 MG A 223 PO4 A 225 HOH A 307 SITE 2 AC4 7 HOH A 337 HOH A 539 HOH A 540 SITE 1 AC5 15 THR A 9 LYS A 13 LYS A 35 ASP A 50 SITE 2 AC5 15 GLU A 116 ALA A 118 GLY A 119 8AC A 221 SITE 3 AC5 15 ADP A 222 MG A 223 MG A 224 HOH A 307 SITE 4 AC5 15 HOH A 337 HOH A 496 HOH A 539 SITE 1 AC6 3 ASN A 130 ASP A 133 HOH A 530 SITE 1 AC7 7 PHE A 72 TYR A 73 ARG A 74 TYR A 75 SITE 2 AC7 7 ASP A 89 HOH A 568 HOH A 569 SITE 1 AC8 6 VAL A 41 ASN A 42 ASP A 43 ARG A 74 SITE 2 AC8 6 HIS A 76 HOH A 577 SITE 1 AC9 5 ASN A 25 LYS A 30 LEU A 61 HOH A 514 SITE 2 AC9 5 HOH A 534 SITE 1 BC1 6 HIS A 0 MET A 1 LYS A 139 LYS A 141 SITE 2 BC1 6 SER A 220 HOH A 578 CRYST1 81.526 37.967 68.795 90.00 101.15 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 0.012266 0.000000 0.002418 0.00000 SCALE2 0.000000 0.026339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014816 0.00000