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 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 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