HEADER LIGASE 15-OCT-98 1BYI TITLE STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DETHIOBIOTIN SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.3.3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS BIOTIN SYNTHESIS, CYCLO-LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SANDALOVA,G.SCHNEIDER,H.KAECK,Y.LINDQVIST REVDAT 4 09-AUG-23 1BYI 1 REMARK REVDAT 3 13-JUL-11 1BYI 1 VERSN REVDAT 2 24-FEB-09 1BYI 1 VERSN REVDAT 1 15-JUN-99 1BYI 0 JRNL AUTH T.SANDALOVA,G.SCHNEIDER,H.KACK,Y.LINDQVIST JRNL TITL STRUCTURE OF DETHIOBIOTIN SYNTHETASE AT 0.97 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 610 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089457 JRNL DOI 10.1107/S090744499801381X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.HUANG,Y.LINDQVIST,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 A RESOLUTION REMARK 1 REF STRUCTURE V. 2 407 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 116232 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.112 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 106843 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 : 0 REMARK 3 SOLVENT ATOMS : 403 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2075.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1684.4 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 79 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 20493 REMARK 3 NUMBER OF RESTRAINTS : 25635 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.149 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.078 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.109 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.075 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.047 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.089 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BYI 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_1000172150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9082 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116232 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 54.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24500 REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL-97, X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1DTS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 36.22350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.90600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.22350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.90600 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 541 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 581 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 582 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 656 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 697 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 10 N - CA - CB ANGL. DEV. = 13.7 DEGREES REMARK 500 ASP A 10 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 ASP A 10 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ASP A 10 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 GLU A 44 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 60 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 PHE A 76 O - C - N ANGL. DEV. = -11.8 DEGREES REMARK 500 GLN A 88 CB - CG - CD ANGL. DEV. = 19.4 DEGREES REMARK 500 GLU A 89 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 MET A 156 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 LYS A 182 CD - CE - NZ ANGL. DEV. = 17.6 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 193 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ALA A 213 N - CA - CB ANGL. DEV. = 9.4 DEGREES 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 THR A 11 137.91 -37.77 REMARK 500 PRO A 79 35.22 -84.09 REMARK 500 PHE A 121 35.48 -95.42 REMARK 500 ALA A 207 48.81 34.05 REMARK 500 GLU A 208 -0.14 79.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE A 121 -13.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BYI 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 FORMUL 2 HOH *403(H2 O) HELIX 1 1 LYS A 15 ALA A 28 1 14 HELIX 2 2 SER A 53 ARG A 60 1 8 HELIX 3 3 TYR A 68 VAL A 71 1 4 HELIX 4 4 PRO A 82 GLU A 89 1 8 HELIX 5 5 SER A 95 GLN A 107 1 13 HELIX 6 6 PHE A 130 GLU A 137 1 8 HELIX 7 7 CYS A 151 HIS A 164 1 14 HELIX 8 8 HIS A 184 MET A 194 1 11 HELIX 9 9 ALA A 207 ASN A 209 5 3 HELIX 10 10 GLY A 216 TYR A 218 5 3 SHEET 1 A 6 LEU A 199 ILE A 203 0 SHEET 2 A 6 LEU A 169 ASN A 175 1 N TRP A 172 O LEU A 200 SHEET 3 A 6 PRO A 140 GLY A 146 1 N VAL A 141 O ALA A 170 SHEET 4 A 6 LYS A 2 GLY A 8 1 N PHE A 5 O PRO A 140 SHEET 5 A 6 TRP A 111 GLU A 115 1 N VAL A 112 O LYS A 2 SHEET 6 A 6 THR A 33 TYR A 36 1 N ALA A 34 O TRP A 111 SHEET 1 B 2 VAL A 39 SER A 41 0 SHEET 2 B 2 TYR A 74 PHE A 76 1 N TYR A 74 O ALA A 40 SHEET 1 C 2 SER A 43 THR A 46 0 SHEET 2 C 2 GLY A 49 ASN A 52 -1 N ARG A 51 O GLU A 44 CRYST1 72.447 47.812 61.202 90.00 107.24 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 0.013803 0.000000 0.004283 0.00000 SCALE2 0.000000 0.020915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017108 0.00000