HEADER FATTY ACID BIOSYNTHESIS 08-JAN-96 1MKB TITLE ESCHERICHIA COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE AT PH 5 TITLE 2 AND 21 DEGREES C COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA-HYDROXYDECANOYL ACP DEHYDRASE; COMPND 5 EC: 4.2.1.60; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: RA244; SOURCE 5 GENE: FABA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRA244; SOURCE 10 EXPRESSION_SYSTEM_GENE: FABA; SOURCE 11 OTHER_DETAILS: TAC PROMOTER KEYWDS FATTY ACID BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.LEESONG REVDAT 3 14-FEB-24 1MKB 1 REMARK REVDAT 2 24-FEB-09 1MKB 1 VERSN REVDAT 1 11-JUL-96 1MKB 0 JRNL AUTH M.LEESONG,B.S.HENDERSON,J.R.GILLIG,J.M.SCHWAB,J.L.SMITH JRNL TITL STRUCTURE OF A DEHYDRATASE-ISOMERASE FROM THE BACTERIAL JRNL TITL 2 PATHWAY FOR BIOSYNTHESIS OF UNSATURATED FATTY ACIDS: TWO JRNL TITL 3 CATALYTIC ACTIVITIES IN ONE ACTIVE SITE. JRNL REF STRUCTURE V. 4 253 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8805534 JRNL DOI 10.1016/S0969-2126(96)00030-5 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 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 : 20804 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) : 0.183 REMARK 3 FREE R VALUE : 0.243 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 : 2650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.80 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: REMARK 3 RESIDUES B 136 - B 137 FORM A POORLY ORDERED LOOP AND REMARK 3 HAVE HIGH ISOTROPIC B-FACTORS. REMARK 4 REMARK 4 1MKB 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_1000175036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21621 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06300 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: 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 34.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.45000 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: 3200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A 74 62.08 -158.15 REMARK 500 ARG A 136 -135.76 -99.66 REMARK 500 THR B 45 -169.39 -128.99 REMARK 500 ASP B 74 68.94 -156.53 REMARK 500 ASN B 135 40.40 -95.35 REMARK 500 ARG B 136 -154.52 -89.66 REMARK 500 LEU B 138 83.98 155.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: TWO POLAR RESIDUES ARE FOUND IN THE CATALYTIC REMARK 800 REGION OF THE ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: TWO POLAR RESIDUES ARE FOUND IN THE CATALYTIC REMARK 800 REGION OF THE ACTIVE SITE. DBREF 1MKB A 1 171 UNP P0A6Q3 FABA_ECOLI 1 171 DBREF 1MKB B 1 171 UNP P0A6Q3 FABA_ECOLI 1 171 SEQRES 1 A 171 VAL ASP LYS ARG GLU SER TYR THR LYS GLU ASP LEU LEU SEQRES 2 A 171 ALA SER GLY ARG GLY GLU LEU PHE GLY ALA LYS GLY PRO SEQRES 3 A 171 GLN LEU PRO ALA PRO ASN MET LEU MET MET ASP ARG VAL SEQRES 4 A 171 VAL LYS MET THR GLU THR GLY GLY ASN PHE ASP LYS GLY SEQRES 5 A 171 TYR VAL GLU ALA GLU LEU ASP ILE ASN PRO ASP LEU TRP SEQRES 6 A 171 PHE PHE GLY CYS HIS PHE ILE GLY ASP PRO VAL MET PRO SEQRES 7 A 171 GLY CYS LEU GLY LEU ASP ALA MET TRP GLN LEU VAL GLY SEQRES 8 A 171 PHE TYR LEU GLY TRP LEU GLY GLY GLU GLY LYS GLY ARG SEQRES 9 A 171 ALA LEU GLY VAL GLY GLU VAL LYS PHE THR GLY GLN VAL SEQRES 10 A 171 LEU PRO THR ALA LYS LYS VAL THR TYR ARG ILE HIS PHE SEQRES 11 A 171 LYS ARG ILE VAL ASN ARG ARG LEU ILE MET GLY LEU ALA SEQRES 12 A 171 ASP GLY GLU VAL LEU VAL ASP GLY ARG LEU ILE TYR THR SEQRES 13 A 171 ALA SER ASP LEU LYS VAL GLY LEU PHE GLN ASP THR SER SEQRES 14 A 171 ALA PHE SEQRES 1 B 171 VAL ASP LYS ARG GLU SER TYR THR LYS GLU ASP LEU LEU SEQRES 2 B 171 ALA SER GLY ARG GLY GLU LEU PHE GLY ALA LYS GLY PRO SEQRES 3 B 171 GLN LEU PRO ALA PRO ASN MET LEU MET MET ASP ARG VAL SEQRES 4 B 171 VAL LYS MET THR GLU THR GLY GLY ASN PHE ASP LYS GLY SEQRES 5 B 171 TYR VAL GLU ALA GLU LEU ASP ILE ASN PRO ASP LEU TRP SEQRES 6 B 171 PHE PHE GLY CYS HIS PHE ILE GLY ASP PRO VAL MET PRO SEQRES 7 B 171 GLY CYS LEU GLY LEU ASP ALA MET TRP GLN LEU VAL GLY SEQRES 8 B 171 PHE TYR LEU GLY TRP LEU GLY GLY GLU GLY LYS GLY ARG SEQRES 9 B 171 ALA LEU GLY VAL GLY GLU VAL LYS PHE THR GLY GLN VAL SEQRES 10 B 171 LEU PRO THR ALA LYS LYS VAL THR TYR ARG ILE HIS PHE SEQRES 11 B 171 LYS ARG ILE VAL ASN ARG ARG LEU ILE MET GLY LEU ALA SEQRES 12 B 171 ASP GLY GLU VAL LEU VAL ASP GLY ARG LEU ILE TYR THR SEQRES 13 B 171 ALA SER ASP LEU LYS VAL GLY LEU PHE GLN ASP THR SER SEQRES 14 B 171 ALA PHE FORMUL 3 HOH *163(H2 O) HELIX 1 1 LYS A 9 ARG A 17 1 9 HELIX 2 2 TRP A 65 CYS A 69 1 5 HELIX 3 3 GLY A 79 TRP A 96 1 18 HELIX 4 4 THR A 168 ALA A 170 5 3 HELIX 5 5 LYS B 9 ARG B 17 1 9 HELIX 6 6 TRP B 65 CYS B 69 1 5 HELIX 7 7 GLY B 79 TRP B 96 1 18 SHEET 1 A14 GLU A 5 LYS A 9 0 SHEET 2 A14 ASP A 37 THR A 43 -1 N MET A 42 O GLU A 5 SHEET 3 A14 GLY A 52 ILE A 60 -1 N TYR A 53 O THR A 43 SHEET 4 A14 LYS A 122 ARG A 136 -1 N PHE A 130 O GLY A 52 SHEET 5 A14 LEU A 138 ASP A 150 -1 N ASP A 150 O LYS A 123 SHEET 6 A14 ARG A 152 PHE A 165 -1 N ARG A 152 O VAL A 149 SHEET 7 A14 LYS A 102 THR A 114 -1 N THR A 114 O ILE A 154 SHEET 8 A14 LYS B 102 THR B 114 -1 N PHE B 113 O LEU A 106 SHEET 9 A14 ARG B 152 PHE B 165 -1 N PHE B 165 O LYS B 102 SHEET 10 A14 LEU B 138 ASP B 150 -1 N VAL B 149 O ARG B 152 SHEET 11 A14 LYS B 122 ARG B 136 -1 N ARG B 136 O LEU B 138 SHEET 12 A14 GLY B 52 ILE B 60 -1 N ILE B 60 O LYS B 122 SHEET 13 A14 ASP B 37 THR B 43 -1 N ASP B 37 O GLU B 57 SHEET 14 A14 GLU B 5 LYS B 9 -1 N LYS B 9 O ASP B 37 CISPEP 1 PRO A 31 ASN A 32 0 2.11 CISPEP 2 HIS A 70 PHE A 71 0 -1.08 CISPEP 3 PRO B 31 ASN B 32 0 0.90 CISPEP 4 HIS B 70 PHE B 71 0 -0.70 SITE 1 AC1 2 HIS A 70 ASP B 84 SITE 1 AC2 2 HIS B 70 ASP A 84 CRYST1 68.500 86.900 60.500 90.00 90.00 90.00 P 21 21 21 8 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 0.014599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016529 0.00000 MTRIX1 1 -0.935900 0.159000 -0.314300 -11.66340 1 MTRIX2 1 0.159700 -0.603800 -0.780900 24.64240 1 MTRIX3 1 -0.314000 -0.781100 0.539800 10.02840 1