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HEADER TRANSFERASE 21-NOV-95 1BDO TITLE STRUCTURE OF THE BIOTINYL DOMAIN OF ACETYL-COENZYME A TITLE 2 CARBOXYLASE DETERMINED BY MAD PHASING COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETYL-COA CARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BIOTINYL DOMAIN, RESIDUES 77 - 156; COMPND 5 SYNONYM: FUNCTIONAL FRAGMENT OF BIOTIN CARBOXYL CARRIER COMPND 6 PROTEIN, BCCPSC; COMPND 7 EC: 6.4.1.2; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: BCCPSC IS OBTAINED BY DIGESTING RECOMBINANT COMPND 10 BIOTIN CARBOXYL CARRIER PROTEIN WITH SUBTILISIN CARLSBERG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 GENE: BIOTIN CARBOXYL CARRIER PROTEI; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PRSETB; SOURCE 7 EXPRESSION_SYSTEM_GENE: BIOTIN CARBOXYL CARRIER PROTEIN; SOURCE 8 OTHER_DETAILS: THE FRAGMENT BCCPSC, RESIDUES 77-156, IS SOURCE 9 OBTAINED BY DIGESTING THE EXPRESSED RECOMBINANT PROTEIN SOURCE 10 WITH SUBTILISIN CARLSBERG KEYWDS BCCPSC, CARBOXYL TRANSFERASE, FATTY ACID BIOSYNTHESIS, KEYWDS 2 HAMMERHEAD STRUCTURE, SELENOMETHIONINE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR F.K.ATHAPPILLY,W.A.HENDRICKSON REVDAT 2 01-APR-03 1BDO 1 JRNL REVDAT 1 01-AUG-96 1BDO 0 JRNL AUTH F.K.ATHAPPILLY,W.A.HENDRICKSON JRNL TITL STRUCTURE OF THE BIOTINYL DOMAIN OF JRNL TITL 2 ACETYL-COENZYME A CARBOXYLASE DETERMINED BY MAD JRNL TITL 3 PHASING. JRNL REF STRUCTURE V. 3 1407 1995 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 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) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 14311 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) : 0.189 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 : 615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.00 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.54 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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) : 1.900 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 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 : ENGH AND HUBER (1991) REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BDO COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-16) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-1993 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9803 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : FUJI BAS-2000 IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14891 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: A MODIFIED MAD REMARK 200 PROCEDURE. SOFTWARE USED : NULL STARTING MODEL FOR MOLECULAR REMARK 200 REPLACEMENT: 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 (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 1/2-X,1/2+Y,-Z REMARK 290 4555 1/2+X,1/2-Y,-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 32.73000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.73000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.63000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 37.26000 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 201 LIES ON A SPECIAL POSITION. 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 87 SD MET A 87 CE -0.056 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 118 N - CA - C ANGL. DEV. = -9.7 DEGREES REMARK 500 MET A 123 N - CA - C ANGL. DEV. = -9.4 DEGREES REMARK 500 ILE A 138 N - CA - C ANGL. DEV. = -9.6 DEGREES REMARK 500 LEU A 139 N - CA - C ANGL. DEV. = 9.1 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 220 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH 340 DISTANCE = 6.50 ANGSTROMS DBREF 1BDO A 77 156 UNP P0ABD8 BCCP_ECOLI 77 156 SEQRES 1 A 80 GLU ILE SER GLY HIS ILE VAL ARG SER PRO MET VAL GLY SEQRES 2 A 80 THR PHE TYR ARG THR PRO SER PRO ASP ALA LYS ALA PHE SEQRES 3 A 80 ILE GLU VAL GLY GLN LYS VAL ASN VAL GLY ASP THR LEU SEQRES 4 A 80 CYS ILE VAL GLU ALA MET LYS MET MET ASN GLN ILE GLU SEQRES 5 A 80 ALA ASP LYS SER GLY THR VAL LYS ALA ILE LEU VAL GLU SEQRES 6 A 80 SER GLY GLN PRO VAL GLU PHE ASP GLU PRO LEU VAL VAL SEQRES 7 A 80 ILE GLU HET BTN 122 15 HETNAM BTN BIOTIN FORMUL 2 BTN C10 H16 N2 O3 S FORMUL 3 HOH *74(H2 O) SHEET 1 A 3 THR A 90 TYR A 92 0 SHEET 2 A 3 THR A 114 ALA A 120 -1 N GLU A 119 O THR A 90 SHEET 3 A 3 MET A 123 GLU A 128 -1 N ILE A 127 O LEU A 115 SHEET 1 B 3 HIS A 81 ARG A 84 0 SHEET 2 B 3 PRO A 151 ILE A 155 -1 N ILE A 155 O HIS A 81 SHEET 3 B 3 VAL A 135 ILE A 138 -1 N ALA A 137 O VAL A 154 LINK C11 BTN 122 NZ LYS A 122 CRYST1 65.460 37.260 35.450 90.00 90.00 90.00 P 21 21 2 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 0.015277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028209 0.00000