HEADER ACYLTRANSFERASE 22-DEC-97 1KAS
TITLE BETA-KETOACYL-ACP SYNTHASE II FROM ESCHERICHIA COLI
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-KETOACYL ACP SYNTHASE II;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.3.1.41;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562
KEYWDS ACYLTRANSFERASE, CONDENSING ENZYME, FATTY ACID ELONGATION, LIPID
KEYWDS 2 METABOLISM, ALPHA-BETA PROTEIN, FIVE-LAYERED FOLD, ALPHA-BETA-ALPHA-
KEYWDS 3 BETA-ALPHA
EXPDTA X-RAY DIFFRACTION
AUTHOR W.HUANG,J.JIA,P.EDWARDS,K.DEHESH,G.SCHNEIDER,Y.LINDQVIST
REVDAT 5 07-FEB-24 1KAS 1 REMARK
REVDAT 4 13-JUL-11 1KAS 1 VERSN
REVDAT 3 24-FEB-09 1KAS 1 VERSN
REVDAT 2 20-APR-99 1KAS 1 COMPND REMARK SOURCE JRNL
REVDAT 2 2 1 KEYWDS
REVDAT 1 02-MAR-99 1KAS 0
JRNL AUTH W.HUANG,J.JIA,P.EDWARDS,K.DEHESH,G.SCHNEIDER,Y.LINDQVIST
JRNL TITL CRYSTAL STRUCTURE OF BETA-KETOACYL-ACYL CARRIER PROTEIN
JRNL TITL 2 SYNTHASE II FROM E.COLI REVEALS THE MOLECULAR ARCHITECTURE
JRNL TITL 3 OF CONDENSING ENZYMES.
JRNL REF EMBO J. V. 17 1183 1998
JRNL REFN ISSN 0261-4189
JRNL PMID 9482715
JRNL DOI 10.1093/EMBOJ/17.5.1183
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5
REMARK 3 NUMBER OF REFLECTIONS : 18580
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.242
REMARK 3 R VALUE (WORKING SET) : 0.234
REMARK 3 FREE R VALUE : 0.279
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1810
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3004
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 31
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): NULL
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.004 ; NULL
REMARK 3 ANGLE DISTANCE (A) : 0.018 ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KAS 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_1000174390.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : MAY-97
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 4
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : BW7B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.1050
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18580
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 8.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5
REMARK 200 DATA REDUNDANCY : 7.600
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.27100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: CCP4
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): 2.80
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.94333
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.88667
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.88667
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.94333
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: 5950 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 26380 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 -0.500000 0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 1
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 ALA A 162 -126.00 48.11
REMARK 500 LYS A 192 75.18 -156.11
REMARK 500 TRP A 222 -1.08 74.40
REMARK 500 ALA A 235 132.94 -171.71
REMARK 500 ALA A 255 -178.28 175.89
REMARK 500 TYR A 267 -74.27 -136.76
REMARK 500 SER A 306 29.59 86.00
REMARK 500 LEU A 342 -107.29 42.59
REMARK 500 ASP A 376 -1.71 -150.65
REMARK 500 HIS A 382 -31.48 -130.15
REMARK 500 SER A 388 -54.78 -120.95
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ACT
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: ACTIVE SITE RESIDUE.
DBREF 1KAS A 1 412 UNP P0AAI5 FABF_ECOLI 1 412
SEQRES 1 A 412 SER LYS ARG ARG VAL VAL VAL THR GLY LEU GLY MET LEU
SEQRES 2 A 412 SER PRO VAL GLY ASN THR VAL GLU SER THR TRP LYS ALA
SEQRES 3 A 412 LEU LEU ALA GLY GLN SER GLY ILE SER LEU ILE ASP HIS
SEQRES 4 A 412 PHE ASP THR SER ALA TYR ALA THR LYS PHE ALA GLY LEU
SEQRES 5 A 412 VAL LYS ASP PHE ASN CYS GLU ASP ILE ILE SER ARG LYS
SEQRES 6 A 412 GLU GLN ARG LYS MET ASP ALA PHE ILE GLN TYR GLY ILE
SEQRES 7 A 412 VAL ALA GLY VAL GLN ALA MET GLN ASP SER GLY LEU GLU
SEQRES 8 A 412 ILE THR GLU GLU ASN ALA THR ARG ILE GLY ALA ALA ILE
SEQRES 9 A 412 GLY SER GLY ILE GLY GLY LEU GLY LEU ILE GLU GLU ASN
SEQRES 10 A 412 HIS THR SER LEU MET ASN GLY GLY PRO ARG LYS ILE SER
SEQRES 11 A 412 PRO PHE PHE VAL PRO SER THR ILE VAL ASN MET VAL ALA
SEQRES 12 A 412 GLY HIS LEU THR ILE MET TYR GLY LEU ARG GLY PRO SER
SEQRES 13 A 412 ILE SER ILE ALA THR ALA CYS THR SER GLY VAL HIS ASN
SEQRES 14 A 412 ILE GLY HIS ALA ALA ARG ILE ILE ALA TYR GLY ASP ALA
SEQRES 15 A 412 ASP VAL MET VAL ALA GLY GLY ALA GLU LYS ALA SER THR
SEQRES 16 A 412 PRO LEU GLY VAL GLY GLY PHE GLY ALA ALA ARG ALA LEU
SEQRES 17 A 412 SER THR ARG ASN ASP ASN PRO GLN ALA ALA SER ARG PRO
SEQRES 18 A 412 TRP ASP LYS GLU ARG ASP GLY PHE VAL LEU GLY ASP GLY
SEQRES 19 A 412 ALA GLY MET LEU VAL LEU GLU GLU TYR GLU HIS ALA LYS
SEQRES 20 A 412 LYS ARG GLY ALA LYS ILE TYR ALA GLU LEU VAL GLY PHE
SEQRES 21 A 412 GLY MET SER SER ASP ALA TYR HIS MET THR SER PRO PRO
SEQRES 22 A 412 GLU ASN GLY ALA GLY ALA ALA LEU ALA MET ALA ASN ALA
SEQRES 23 A 412 LEU ARG ASP ALA GLY ILE GLU ALA SER GLN ILE GLY TYR
SEQRES 24 A 412 VAL ASN ALA HIS GLY THR SER THR PRO ALA GLY ASP LYS
SEQRES 25 A 412 ALA GLU ALA GLN ALA VAL LYS THR ILE PHE GLY GLU ALA
SEQRES 26 A 412 ALA SER ARG VAL LEU VAL SER SER THR LYS SER MET THR
SEQRES 27 A 412 GLY HIS LEU LEU GLY ALA ALA GLY ALA VAL GLU SER ILE
SEQRES 28 A 412 TYR SER ILE LEU ALA LEU ARG ASP GLN ALA VAL PRO PRO
SEQRES 29 A 412 THR ILE ASN LEU ASP ASN PRO ASP GLU GLY CYS ASP LEU
SEQRES 30 A 412 ASP PHE VAL PRO HIS GLU ALA ARG GLN VAL SER GLY MET
SEQRES 31 A 412 GLU TYR THR LEU CYS ASN SER PHE GLY PHE GLY GLY THR
SEQRES 32 A 412 ASN GLY SER LEU ILE PHE LYS LYS ILE
FORMUL 2 HOH *31(H2 O)
HELIX 1 1 VAL A 20 LEU A 28 1 9
HELIX 2 2 ARG A 64 LYS A 69 1 6
HELIX 3 3 ALA A 72 SER A 88 1 17
HELIX 4 4 ALA A 97 ARG A 99 5 3
HELIX 5 5 LEU A 111 GLY A 124 1 14
HELIX 6 6 PRO A 126 LYS A 128 5 3
HELIX 7 7 PHE A 133 THR A 137 1 5
HELIX 8 8 VAL A 139 TYR A 150 5 12
HELIX 9 9 ALA A 162 TYR A 179 5 18
HELIX 10 10 PRO A 196 ALA A 204 1 9
HELIX 11 11 PRO A 215 ALA A 218 1 4
HELIX 12 12 TYR A 243 ARG A 249 1 7
HELIX 13 13 ALA A 277 ALA A 290 1 14
HELIX 14 14 ALA A 294 GLN A 296 5 3
HELIX 15 15 PRO A 308 PHE A 322 1 15
HELIX 16 16 THR A 334 THR A 338 5 5
HELIX 17 17 LEU A 342 ASP A 359 5 18
SHEET 1 A 9 ILE A 100 GLY A 105 0
SHEET 2 A 9 VAL A 184 GLU A 191 1 N VAL A 184 O GLY A 101
SHEET 3 A 9 GLY A 234 GLU A 242 -1 N LEU A 240 O MET A 185
SHEET 4 A 9 VAL A 5 LEU A 13 -1 N LEU A 13 O ALA A 235
SHEET 5 A 9 ALA A 255 SER A 264 -1 N LEU A 257 O VAL A 5
SHEET 6 A 9 THR A 403 LYS A 410 -1 N LYS A 410 O GLU A 256
SHEET 7 A 9 TYR A 392 GLY A 399 -1 N GLY A 399 O THR A 403
SHEET 8 A 9 ILE A 297 ASN A 301 1 N GLY A 298 O TYR A 392
SHEET 9 A 9 LEU A 330 SER A 332 1 N LEU A 330 O VAL A 300
SHEET 1 B 2 ILE A 34 LEU A 36 0
SHEET 2 B 2 PHE A 49 GLY A 51 -1 N ALA A 50 O SER A 35
SITE 1 ACT 1 CYS A 163
CRYST1 76.410 76.410 146.830 90.00 90.00 120.00 P 31 2 1 6
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 0.013087 0.007556 0.000000 0.00000
SCALE2 0.000000 0.015112 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006811 0.00000
(ATOM LINES ARE NOT SHOWN.)
END