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HEADER HYDROLASE 07-AUG-09 3ILS
TITLE THE THIOESTERASE DOMAIN FROM PKSA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: AFLATOXIN BIOSYNTHESIS POLYKETIDE SYNTHASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: PKSA THIOESTERASE DOMAIN RESIDUES 1845-2109;
COMPND 5 SYNONYM: PKS;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS PARASITICUS;
SOURCE 3 ORGANISM_TAXID: 5067;
SOURCE 4 GENE: PKSA, PKSL1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS A/B HYDROLASE, THIOESTERASE, NORSOLORINIC ACID, AFLATOXIN,
KEYWDS 2 PKSA, POLYKETIDE, ACYLTRANSFERASE, MULTIFUNCTIONAL ENZYME,
KEYWDS 3 PHOSPHOPANTETHEINE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.P.KORMAN
REVDAT 1 07-APR-10 3ILS 0
JRNL AUTH T.P.KORMAN,J.M.CRAWFORD,J.W.LABONTE,A.G.NEWMAN,
JRNL AUTH 2 J.WONG,C.A.TOWNSEND,S.C.TSAI
JRNL TITL STRUCTURE AND FUNCTION OF AN ITERATIVE POLYKETIDE
JRNL TITL 2 SYNTHASE THIOESTERASE DOMAIN CATALYZING CLAISEN
JRNL TITL 3 CYCLIZATION IN AFLATOXIN BIOSYNTHESIS.
JRNL REF PROC.NATL.ACAD.SCI.USA 2010
JRNL REFN ESSN 1091-6490
JRNL PMID 20332208
JRNL DOI 10.1073/PNAS.0913531107
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 305.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 33560
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) : 0.178
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1662
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 : 2042
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 171
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 4.44000
REMARK 3 B22 (A**2) : 0.73200
REMARK 3 B33 (A**2) : -5.17200
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
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) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
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) : 1.005 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.445 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.552 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.133 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : 39.88
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 : CNS_TOPPAR:PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3ILS COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-09.
REMARK 100 THE RCSB ID CODE IS RCSB054570.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-APR-07; 23-FEB-07
REMARK 200 TEMPERATURE (KELVIN) : 100; NULL
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y; Y
REMARK 200 RADIATION SOURCE : SSRL; ALS
REMARK 200 BEAMLINE : BL9-2; 5.0.2
REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9648, 0.98, 0.9802; 1.0
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111);
REMARK 200 DOUBLE CRYSTAL SI(111)
REMARK 200 OPTICS : NULL; NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD; CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; MARMOSAIC
REMARK 200 325 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35395
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : 0.05700
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 13.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5
REMARK 200 DATA REDUNDANCY IN SHELL : 5.30
REMARK 200 R MERGE FOR SHELL (I) : 0.33000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M
REMARK 280 SODIUM CITRATE, 30% PEG 4K, PH 5.6, VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 33.46700
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.96250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.47050
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.96250
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.46700
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.47050
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 GLN A1858 149.84 -170.29
REMARK 500 MET A1862 -41.31 73.99
REMARK 500 ASP A1903 62.45 -152.82
REMARK 500 SER A1937 -126.83 55.50
REMARK 500 ASP A1964 71.78 41.97
REMARK 500 GLN A1969 148.72 -172.18
REMARK 500
REMARK 500 REMARK: NULL
DBREF 3ILS A 1845 2109 UNP Q12053 PKSL1_ASPPA 1845 2109
SEQRES 1 A 265 LEU LYS PRO TYR CYS ARG PRO SER THR SER VAL VAL LEU
SEQRES 2 A 265 GLN GLY LEU PRO MET VAL ALA ARG LYS THR LEU PHE MET
SEQRES 3 A 265 LEU PRO ASP GLY GLY GLY SER ALA PHE SER TYR ALA SER
SEQRES 4 A 265 LEU PRO ARG LEU LYS SER ASP THR ALA VAL VAL GLY LEU
SEQRES 5 A 265 ASN CYS PRO TYR ALA ARG ASP PRO GLU ASN MET ASN CYS
SEQRES 6 A 265 THR HIS GLY ALA MET ILE GLU SER PHE CYS ASN GLU ILE
SEQRES 7 A 265 ARG ARG ARG GLN PRO ARG GLY PRO TYR HIS LEU GLY GLY
SEQRES 8 A 265 TRP SER SER GLY GLY ALA PHE ALA TYR VAL VAL ALA GLU
SEQRES 9 A 265 ALA LEU VAL ASN GLN GLY GLU GLU VAL HIS SER LEU ILE
SEQRES 10 A 265 ILE ILE ASP ALA PRO ILE PRO GLN ALA MET GLU GLN LEU
SEQRES 11 A 265 PRO ARG ALA PHE TYR GLU HIS CYS ASN SER ILE GLY LEU
SEQRES 12 A 265 PHE ALA THR GLN PRO GLY ALA SER PRO ASP GLY SER THR
SEQRES 13 A 265 GLU PRO PRO SER TYR LEU ILE PRO HIS PHE THR ALA VAL
SEQRES 14 A 265 VAL ASP VAL MET LEU ASP TYR LYS LEU ALA PRO LEU HIS
SEQRES 15 A 265 ALA ARG ARG MET PRO LYS VAL GLY ILE VAL TRP ALA ALA
SEQRES 16 A 265 ASP THR VAL MET ASP GLU ARG ASP ALA PRO LYS MET LYS
SEQRES 17 A 265 GLY MET HIS PHE MET ILE GLN LYS ARG THR GLU PHE GLY
SEQRES 18 A 265 PRO ASP GLY TRP ASP THR ILE MET PRO GLY ALA SER PHE
SEQRES 19 A 265 ASP ILE VAL ARG ALA ASP GLY ALA ASN HIS PHE THR LEU
SEQRES 20 A 265 MET GLN LYS GLU HIS VAL SER ILE ILE SER ASP LEU ILE
SEQRES 21 A 265 ASP ARG VAL MET ALA
FORMUL 2 HOH *171(H2 O)
HELIX 1 1 SER A 1877 ALA A 1882 5 6
HELIX 2 2 ASP A 1903 MET A 1907 5 5
HELIX 3 3 THR A 1910 GLN A 1926 1 17
HELIX 4 4 SER A 1937 GLN A 1953 1 17
HELIX 5 5 PRO A 1975 ILE A 1985 1 11
HELIX 6 6 TYR A 2005 MET A 2017 1 13
HELIX 7 7 GLY A 2068 MET A 2073 1 6
HELIX 8 8 PHE A 2089 GLN A 2093 5 5
HELIX 9 9 VAL A 2097 MET A 2108 1 12
SHEET 1 A 7 THR A1853 GLN A1858 0
SHEET 2 A 7 THR A1891 ASN A1897 -1 O VAL A1893 N GLN A1858
SHEET 3 A 7 LYS A1866 LEU A1871 1 N LEU A1868 O ALA A1892
SHEET 4 A 7 TYR A1931 TRP A1936 1 O GLY A1934 N LEU A1871
SHEET 5 A 7 VAL A1957 ILE A1963 1 O ILE A1963 N GLY A1935
SHEET 6 A 7 LYS A2032 ASP A2040 1 O GLY A2034 N ILE A1962
SHEET 7 A 7 PHE A2078 ASN A2087 1 O ASP A2079 N VAL A2033
CISPEP 1 GLY A 1929 PRO A 1930 0 -7.27
CRYST1 66.934 66.941 67.925 90.00 90.00 90.00 P 21 21 21 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 0.014940 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014939 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014722 0.00000
TER 2043 ALA A2109
MASTER 240 0 0 9 7 0 0 6 2213 1 0 21
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