HEADER BIOTIN BIOSYNTHESIS 29-NOV-94 1DBS TITLE MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE TITLE 2 OF DETHIOBIOTIN SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DETHIOBIOTIN SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.3.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS BIOTIN BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR L.SAWYER,D.ALEXEEV REVDAT 4 07-FEB-24 1DBS 1 REMARK REVDAT 3 29-NOV-17 1DBS 1 HELIX REVDAT 2 24-FEB-09 1DBS 1 VERSN REVDAT 1 20-APR-95 1DBS 0 JRNL AUTH D.ALEXEEV,R.L.BAXTER,L.SAWYER JRNL TITL MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE JRNL TITL 2 STRUCTURE OF DETHIOBIOTIN SYNTHETASE. JRNL REF STRUCTURE V. 2 1061 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 7881906 JRNL DOI 10.1016/S0969-2126(94)00109-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.HUANG,Y.LUNDQUIST,G.SCHNEIDER,K.J.GIBSON,D.FLINT,G.LORIMER REMARK 1 TITL CRYSTAL STRUCTURE OF AN ATP DEPENDENT CARBOXYLASE REMARK 1 TITL 2 DETHIOBIOTIN SYNTHETASE AT 1.65 ANGSTROMS RESOLUTION REMARK 1 REF STRUCTURE V. 2 407 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.ALEXEEV,R.L.BAXTER REMARK 1 TITL SEQUENCE AND CRYSTALLIZATION OF ESCHERICHIA COLI REMARK 1 TITL 2 DETHIOBIOTIN SYNTHETASE, THE PENULTIMATE ENZYME OF BIOTIN REMARK 1 TITL 3 BIOSYNTHESIS REMARK 1 REF J.MOL.BIOL. V. 235 774 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1692 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.070 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.15 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18656 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 7.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 36.43700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.43700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.50000 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 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 55.58446 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.82062 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 GLU A 208 -80.29 -174.95 REMARK 500 ASN A 209 82.39 -174.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HOH 403 MAY BE A SODIUM ION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 DBREF 1DBS A 1 224 UNP P13000 BIOD_ECOLI 1 224 SEQRES 1 A 224 SER LYS ARG TYR PHE VAL THR GLY THR ASP THR GLU VAL SEQRES 2 A 224 GLY LYS THR VAL ALA SER CYS ALA LEU LEU GLN ALA ALA SEQRES 3 A 224 LYS ALA ALA GLY TYR ARG THR ALA GLY TYR LYS PRO VAL SEQRES 4 A 224 ALA SER GLY SER GLU LYS THR PRO GLU GLY LEU ARG ASN SEQRES 5 A 224 SER ASP ALA LEU ALA LEU GLN ARG ASN SER SER LEU GLN SEQRES 6 A 224 LEU ASP TYR ALA THR VAL ASN PRO TYR THR PHE ALA GLU SEQRES 7 A 224 PRO THR SER PRO HIS ILE ILE SER ALA GLN GLU GLY ARG SEQRES 8 A 224 PRO ILE GLU SER LEU VAL MET SER ALA GLY LEU ARG ALA SEQRES 9 A 224 LEU GLU GLN GLN ALA ASP TRP VAL LEU VAL GLU GLY ALA SEQRES 10 A 224 GLY GLY TRP PHE THR PRO LEU SER ASP THR PHE THR PHE SEQRES 11 A 224 ALA ASP TRP VAL THR GLN GLU GLN LEU PRO VAL ILE LEU SEQRES 12 A 224 VAL VAL GLY VAL LYS LEU GLY CYS ILE ASN HIS ALA MET SEQRES 13 A 224 LEU THR ALA GLN VAL ILE GLN HIS ALA GLY LEU THR LEU SEQRES 14 A 224 ALA GLY TRP VAL ALA ASN ASP VAL THR PRO PRO GLY LYS SEQRES 15 A 224 ARG HIS ALA GLU TYR MET THR THR LEU THR ARG MET ILE SEQRES 16 A 224 PRO ALA PRO LEU LEU GLY GLU ILE PRO TRP LEU ALA GLU SEQRES 17 A 224 ASN PRO GLU ASN ALA ALA THR GLY LYS TYR ILE ASN LEU SEQRES 18 A 224 ALA LEU LEU HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *201(H2 O) HELIX 1 A1 LYS A 15 ALA A 29 1 15 HELIX 2 A2 SER A 53 ASN A 61 1 9 HELIX 3 A3 PRO A 82 GLU A 89 1 8 HELIX 4 A4 SER A 95 GLU A 106 1 12 HELIX 5 A5 PHE A 130 GLU A 137 1 8 HELIX 6 A6 CYS A 151 ALA A 165 1 15 HELIX 7 A7 HIS A 184 MET A 194 1 11 SHEET 1 BET 8 LYS A 2 THR A 7 0 SHEET 2 BET 8 THR A 33 TYR A 36 1 SHEET 3 BET 8 PRO A 38 SER A 41 1 SHEET 4 BET 8 TYR A 74 PHE A 76 1 SHEET 5 BET 8 TRP A 111 GLY A 116 1 SHEET 6 BET 8 VAL A 141 VAL A 145 1 SHEET 7 BET 8 TRP A 172 ASN A 175 1 SHEET 8 BET 8 LEU A 200 ILE A 203 1 SITE 1 AC1 8 GLU A 12 VAL A 13 GLY A 14 LYS A 15 SITE 2 AC1 8 HOH A 401 HOH A 402 HOH A 446 HOH A 466 SITE 1 AC2 8 LYS A 15 LYS A 37 ALA A 117 GLY A 118 SITE 2 AC2 8 HOH A 401 HOH A 410 HOH A 446 HOH A 467 SITE 1 AC3 10 SER A 1 ARG A 51 GLN A 59 TYR A 68 SITE 2 AC3 10 HOH A 405 HOH A 434 HOH A 435 HOH A 534 SITE 3 AC3 10 HOH A 591 HOH A 593 CRYST1 72.874 49.000 61.309 90.00 106.38 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 0.013722 0.000000 0.004033 0.00000 SCALE2 0.000000 0.020408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017001 0.00000