HEADER LIGASE 02-MAR-11 3QXX TITLE CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER TITLE 2 PYLORI COMPLEXED WITH GDP 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, STRUCTURAL GENOMICS, PSI-BIOLOGY, KEYWDS 2 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,A.JOACHIMIAK,W.MINOR, AUTHOR 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 13-SEP-23 3QXX 1 REMARK REVDAT 4 13-APR-22 3QXX 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 27-MAR-13 3QXX 1 JRNL REVDAT 2 28-MAR-12 3QXX 1 JRNL VERSN REVDAT 1 30-MAR-11 3QXX 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 (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 41560 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2205 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) : 2679 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1744 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 341 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.70000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71000 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): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.317 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1935 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1294 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2629 ; 1.683 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3198 ; 3.719 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 6.181 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;34.234 ;25.244 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 340 ;11.412 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;18.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 307 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2114 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 361 ; 0.011 ; 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): 1168 ; 2.045 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 467 ; 2.281 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1900 ; 2.784 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 767 ; 4.069 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 722 ; 5.528 ; 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): 1868 ; 2.300 ; 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 3QXX 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_1000064242. 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 : 43768 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 29.5000 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 (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38600 REMARK 200 R SYM FOR SHELL (I) : 0.38600 REMARK 200 FOR SHELL : 2.500 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 (%): 36.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350; 100 MM NH4NO3; 100 MM BIS REMARK 280 -TRIS; 5% GLYCEROL; SOAKED WITH 10 MM GDP, 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 40.94150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.92250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.94150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.92250 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: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 13.48874 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -67.50453 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 380 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 394 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 GLU A 128 CD OE1 OE2 REMARK 470 GLN A 167 CG 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: 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 570 O HOH A 573 2.19 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 ASN A 8 -178.91 -170.84 REMARK 500 ASN A 179 -1.02 84.52 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 224 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 ASP A 50 OD2 80.6 REMARK 620 3 GLU A 116 OE2 84.6 89.5 REMARK 620 4 GDP A 222 O3B 89.9 165.2 101.0 REMARK 620 5 PO4 A 225 O1 170.0 94.8 86.5 96.2 REMARK 620 6 HOH A 517 O 93.1 85.0 174.4 84.1 95.3 REMARK 620 N 1 2 3 4 5 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 GDP A 222 O1B REMARK 620 2 PO4 A 225 O3 104.1 REMARK 620 3 HOH A 269 O 88.0 163.7 REMARK 620 4 HOH A 289 O 168.1 85.1 84.5 REMARK 620 5 HOH A 290 O 93.1 88.8 79.5 94.6 REMARK 620 6 HOH A 517 O 86.1 108.1 83.3 83.8 162.8 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 GDP 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 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 GOL 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: 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: 3QY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM REMARK 900 HELICOBACTER PYLORI COMPLEXED WITH GDP DBREF 3QXX A 1 218 UNP O24872 BIOD_HELPY 1 218 SEQADV 3QXX MET A -21 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLY A -20 UNP O24872 EXPRESSION TAG SEQADV 3QXX SER A -19 UNP O24872 EXPRESSION TAG SEQADV 3QXX SER A -18 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -17 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -16 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -15 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -14 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -13 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A -12 UNP O24872 EXPRESSION TAG SEQADV 3QXX SER A -11 UNP O24872 EXPRESSION TAG SEQADV 3QXX SER A -10 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLY A -9 UNP O24872 EXPRESSION TAG SEQADV 3QXX ARG A -8 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLU A -7 UNP O24872 EXPRESSION TAG SEQADV 3QXX ASN A -6 UNP O24872 EXPRESSION TAG SEQADV 3QXX LEU A -5 UNP O24872 EXPRESSION TAG SEQADV 3QXX TYR A -4 UNP O24872 EXPRESSION TAG SEQADV 3QXX PHE A -3 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLN A -2 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLY A -1 UNP O24872 EXPRESSION TAG SEQADV 3QXX HIS A 0 UNP O24872 EXPRESSION TAG SEQADV 3QXX GLY A 219 UNP O24872 EXPRESSION TAG SEQADV 3QXX 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 GDP A 222 28 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 HET EDO A 231 4 HET GOL A 232 6 HETNAM 8AC 8-AMINOOCTANOIC ACID HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN 8AC 8-AMINOCAPRYLIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 8AC C8 H17 N O2 FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 PO4 O4 P 3- FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *341(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 LEU A 34 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 2.20 LINK OD2 ASP A 50 MG MG A 224 1555 1555 2.11 LINK OE2 GLU A 116 MG MG A 224 1555 1555 2.05 LINK O1B GDP A 222 MG MG A 223 1555 1555 2.01 LINK O3B GDP A 222 MG MG A 224 1555 1555 2.01 LINK MG MG A 223 O3 PO4 A 225 1555 1555 1.97 LINK MG MG A 223 O HOH A 269 1555 1555 2.20 LINK MG MG A 223 O HOH A 289 1555 1555 2.15 LINK MG MG A 223 O HOH A 290 1555 1555 2.13 LINK MG MG A 223 O HOH A 517 1555 1555 2.24 LINK MG MG A 224 O1 PO4 A 225 1555 1555 2.07 LINK MG MG A 224 O HOH A 517 1555 1555 2.19 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 252 HOH A 291 HOH A 293 SITE 4 AC1 13 HOH A 377 SITE 1 AC2 20 ASN A 10 ALA A 11 GLY A 12 LYS A 13 SITE 2 AC2 20 THR A 14 THR A 15 GLU A 116 ASN A 175 SITE 3 AC2 20 LYS A 177 GLY A 178 MG A 223 MG A 224 SITE 4 AC2 20 PO4 A 225 HOH A 261 HOH A 269 HOH A 290 SITE 5 AC2 20 HOH A 303 HOH A 413 HOH A 517 HOH A 534 SITE 1 AC3 7 GDP A 222 MG A 224 PO4 A 225 HOH A 269 SITE 2 AC3 7 HOH A 289 HOH A 290 HOH A 517 SITE 1 AC4 8 THR A 14 LYS A 35 ASP A 50 GLU A 116 SITE 2 AC4 8 GDP A 222 MG A 223 PO4 A 225 HOH A 517 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 GDP A 222 MG A 223 MG A 224 HOH A 255 SITE 4 AC5 15 HOH A 289 HOH A 290 HOH A 493 SITE 1 AC6 4 ASN A 42 ASP A 43 ARG A 74 HIS A 76 SITE 1 AC7 5 HIS A 0 MET A 1 LYS A 139 LYS A 141 SITE 2 AC7 5 SER A 220 SITE 1 AC8 5 LYS A 171 ASN A 200 PRO A 201 HOH A 474 SITE 2 AC8 5 HOH A 511 SITE 1 AC9 7 PHE A 72 TYR A 73 ARG A 74 TYR A 75 SITE 2 AC9 7 ASP A 89 HOH A 314 HOH A 555 SITE 1 BC1 3 GLN A 22 ASP A 57 HOH A 557 SITE 1 BC2 3 TYR A 73 ALA A 92 PRO A 93 SITE 1 BC3 5 ASN A 130 ASP A 133 HIS A 166 HOH A 285 SITE 2 BC3 5 HOH A 397 CRYST1 81.883 37.845 68.839 90.00 101.30 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 0.012213 0.000000 0.002439 0.00000 SCALE2 0.000000 0.026424 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014814 0.00000