HEADER LIGASE 02-MAR-11 3QXS TITLE CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER TITLE 2 PYLORI COMPLEXED WITH ANP 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_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 GENE: BIOD, HP0029, HP_0029; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD(DE3) MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 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 M.M.KLIMECKA,P.J.POREBSKI,M.CHRUSZCZ,K.JABLONSKA,K.MURZYN, AUTHOR 2 A.JOACHIMIAK,W.MINOR,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 13-SEP-23 3QXS 1 REMARK REVDAT 4 13-APR-22 3QXS 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 27-MAR-13 3QXS 1 JRNL REVDAT 2 28-MAR-12 3QXS 1 JRNL VERSN REVDAT 1 30-MAR-11 3QXS 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 42490 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) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2261 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2734 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1750 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.34000 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): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.373 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2000 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1336 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2722 ; 1.834 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3303 ; 2.288 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 260 ; 5.956 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;34.373 ;25.287 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 352 ;11.277 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.193 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2217 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 377 ; 0.006 ; 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): 1206 ; 0.960 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 479 ; 0.186 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1966 ; 1.659 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 794 ; 2.621 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 745 ; 3.777 ; 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 : 6 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 45 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7950 -21.1620 -14.0620 REMARK 3 T TENSOR REMARK 3 T11: 0.0270 T22: 0.0737 REMARK 3 T33: 0.0400 T12: -0.0129 REMARK 3 T13: -0.0044 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.6512 L22: 0.5869 REMARK 3 L33: 0.9608 L12: -0.1704 REMARK 3 L13: -0.2147 L23: 0.0655 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: -0.0574 S13: -0.0324 REMARK 3 S21: 0.0464 S22: 0.0069 S23: -0.0162 REMARK 3 S31: 0.0784 S32: 0.0367 S33: -0.0103 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 46 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3470 -26.2640 -8.2660 REMARK 3 T TENSOR REMARK 3 T11: 0.0481 T22: 0.0797 REMARK 3 T33: 0.0420 T12: -0.0187 REMARK 3 T13: 0.0103 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 1.3672 L22: 0.4558 REMARK 3 L33: 0.8976 L12: -0.2581 REMARK 3 L13: 0.6414 L23: -0.1322 REMARK 3 S TENSOR REMARK 3 S11: 0.0194 S12: -0.1343 S13: -0.1574 REMARK 3 S21: 0.0371 S22: 0.0076 S23: 0.0327 REMARK 3 S31: 0.1601 S32: -0.0510 S33: -0.0269 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 85 A 102 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9070 -15.5950 -10.5500 REMARK 3 T TENSOR REMARK 3 T11: 0.0429 T22: 0.1105 REMARK 3 T33: 0.0630 T12: -0.0317 REMARK 3 T13: 0.0272 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 2.7846 L22: 1.4995 REMARK 3 L33: 1.1227 L12: 1.4345 REMARK 3 L13: 0.6495 L23: 0.7579 REMARK 3 S TENSOR REMARK 3 S11: 0.0747 S12: -0.3271 S13: 0.2636 REMARK 3 S21: 0.2077 S22: -0.2122 S23: 0.2314 REMARK 3 S31: 0.1516 S32: -0.2257 S33: 0.1376 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 103 A 175 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1950 -13.3530 -21.7360 REMARK 3 T TENSOR REMARK 3 T11: 0.0316 T22: 0.0550 REMARK 3 T33: 0.0521 T12: -0.0149 REMARK 3 T13: -0.0032 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.4922 L22: 0.1544 REMARK 3 L33: 0.7217 L12: -0.0804 REMARK 3 L13: 0.1172 L23: 0.0537 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0314 S13: 0.0425 REMARK 3 S21: -0.0005 S22: -0.0060 S23: 0.0105 REMARK 3 S31: -0.0462 S32: -0.0114 S33: -0.0015 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 176 A 203 REMARK 3 ORIGIN FOR THE GROUP (A): 23.2460 -19.9750 -36.5610 REMARK 3 T TENSOR REMARK 3 T11: 0.0287 T22: 0.0846 REMARK 3 T33: 0.0715 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.5365 L22: 1.8561 REMARK 3 L33: 1.7354 L12: 0.3027 REMARK 3 L13: -0.0325 L23: -0.0897 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: 0.0337 S13: 0.0211 REMARK 3 S21: -0.1145 S22: -0.0186 S23: 0.0999 REMARK 3 S31: -0.0171 S32: 0.1288 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 204 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7490 -16.0170 -20.1210 REMARK 3 T TENSOR REMARK 3 T11: 0.0044 T22: 0.0913 REMARK 3 T33: 0.0581 T12: -0.0099 REMARK 3 T13: -0.0011 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.1040 L22: 4.5809 REMARK 3 L33: 3.2401 L12: 0.2196 REMARK 3 L13: -0.0552 L23: 2.3246 REMARK 3 S TENSOR REMARK 3 S11: 0.0471 S12: -0.1280 S13: 0.0826 REMARK 3 S21: 0.0934 S22: 0.0330 S23: -0.1237 REMARK 3 S31: 0.0074 S32: 0.1676 S33: -0.0801 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 3QXS 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_1000064237. 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 : 44773 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 : 3.800 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 46.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.10800 REMARK 200 R SYM FOR SHELL (I) : 0.10800 REMARK 200 FOR SHELL : 10.50 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 (%): 36.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG3350; 100 MM NH4NO3; 100 MM BIS REMARK 280 -TRIS; SOAKED WITH 10 MM ANP, 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 41.04250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.79100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.04250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.79100 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: 7610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 13.54204 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -67.89465 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 353 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 LYS A 139 NZ 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 OE2 -0.096 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 86.1 REMARK 620 3 GLU A 116 OE2 84.2 88.3 REMARK 620 4 ANP A 222 O2G 173.6 95.3 89.6 REMARK 620 5 ANP A 222 O2B 89.2 171.3 98.5 90.1 REMARK 620 6 HOH A 455 O 90.6 85.9 172.4 95.7 86.8 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 EDO A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP 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 EDO A 224 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 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 EDO A 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 234 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: 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 3QXS A 1 218 UNP O24872 BIOD_HELPY 1 218 SEQADV 3QXS MET A -21 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLY A -20 UNP O24872 EXPRESSION TAG SEQADV 3QXS SER A -19 UNP O24872 EXPRESSION TAG SEQADV 3QXS SER A -18 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -17 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -16 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -15 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -14 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -13 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A -12 UNP O24872 EXPRESSION TAG SEQADV 3QXS SER A -11 UNP O24872 EXPRESSION TAG SEQADV 3QXS SER A -10 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLY A -9 UNP O24872 EXPRESSION TAG SEQADV 3QXS ARG A -8 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLU A -7 UNP O24872 EXPRESSION TAG SEQADV 3QXS ASN A -6 UNP O24872 EXPRESSION TAG SEQADV 3QXS LEU A -5 UNP O24872 EXPRESSION TAG SEQADV 3QXS TYR A -4 UNP O24872 EXPRESSION TAG SEQADV 3QXS PHE A -3 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLN A -2 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLY A -1 UNP O24872 EXPRESSION TAG SEQADV 3QXS HIS A 0 UNP O24872 EXPRESSION TAG SEQADV 3QXS GLY A 219 UNP O24872 EXPRESSION TAG SEQADV 3QXS 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 EDO A 221 4 HET ANP A 222 31 HET MG A 223 1 HET EDO A 224 4 HET NO3 A 225 4 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 EDO A 232 4 HET EDO A 233 4 HET EDO A 234 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM NO3 NITRATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 11(C2 H6 O2) FORMUL 3 ANP C10 H17 N6 O12 P3 FORMUL 4 MG MG 2+ FORMUL 6 NO3 N O3 1- FORMUL 16 HOH *316(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 2.11 LINK OD2 ASP A 50 MG MG A 223 1555 1555 2.07 LINK OE2 GLU A 116 MG MG A 223 1555 1555 2.18 LINK O2G ANP A 222 MG MG A 223 1555 1555 1.99 LINK O2B ANP A 222 MG MG A 223 1555 1555 2.06 LINK MG MG A 223 O HOH A 455 1555 1555 2.12 SITE 1 AC1 3 HIS A 147 ASN A 149 HOH A 419 SITE 1 AC2 25 THR A 9 ASN A 10 ALA A 11 GLY A 12 SITE 2 AC2 25 LYS A 13 THR A 14 THR A 15 LYS A 35 SITE 3 AC2 25 ASP A 50 GLU A 116 GLN A 167 ASN A 175 SITE 4 AC2 25 LYS A 177 MG A 223 HOH A 243 HOH A 255 SITE 5 AC2 25 HOH A 286 HOH A 289 HOH A 299 HOH A 302 SITE 6 AC2 25 HOH A 321 HOH A 370 HOH A 437 HOH A 455 SITE 7 AC2 25 HOH A 485 SITE 1 AC3 5 THR A 14 ASP A 50 GLU A 116 ANP A 222 SITE 2 AC3 5 HOH A 455 SITE 1 AC4 5 ASN A 130 LEU A 132 ASP A 133 HIS A 166 SITE 2 AC4 5 EDO A 234 SITE 1 AC5 9 SER A 5 ALA A 6 LYS A 13 GLY A 117 SITE 2 AC5 9 ALA A 118 GLY A 119 GLY A 120 LEU A 121 SITE 3 AC5 9 HOH A 285 SITE 1 AC6 7 PHE A 72 TYR A 73 ARG A 74 TYR A 75 SITE 2 AC6 7 HOH A 294 HOH A 445 HOH A 481 SITE 1 AC7 8 CYS A 122 GLU A 129 ASN A 130 LEU A 157 SITE 2 AC7 8 TYR A 190 EDO A 234 HOH A 392 HOH A 545 SITE 1 AC8 4 ASP A 111 HOH A 305 HOH A 412 HOH A 491 SITE 1 AC9 7 THR A 181 ASN A 195 ASN A 199 ILE A 202 SITE 2 AC9 7 ILE A 204 HOH A 295 HOH A 456 SITE 1 BC1 6 ASN A 42 ASP A 43 ARG A 74 HIS A 76 SITE 2 BC1 6 HOH A 293 HOH A 445 SITE 1 BC2 3 GLN A 22 ASP A 57 HOH A 473 SITE 1 BC3 7 SER A 185 LYS A 210 VAL A 211 SER A 214 SITE 2 BC3 7 HOH A 469 HOH A 522 HOH A 533 SITE 1 BC4 5 HIS A 0 MET A 1 LYS A 139 LYS A 141 SITE 2 BC4 5 SER A 220 SITE 1 BC5 5 GLU A 128 ASN A 130 ASP A 133 EDO A 224 SITE 2 BC5 5 EDO A 227 CRYST1 82.085 37.582 69.232 90.00 101.28 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 0.012182 0.000000 0.002429 0.00000 SCALE2 0.000000 0.026608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014729 0.00000