HEADER TRANSFERASE 06-NOV-14 4RR5 TITLE THE CRYSTAL STRUCTURE OF SYNECHOCYSTIS SP. PCC 6803 MALONYL-COA: ACP TITLE 2 TRANSACYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MCT; COMPND 5 EC: 2.3.1.39; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803 SUBSTR. KAZUSA; SOURCE 3 ORGANISM_TAXID: 1111708; SOURCE 4 GENE: FABD, SLR2023; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU REVDAT 2 08-NOV-23 4RR5 1 REMARK REVDAT 1 01-JUL-15 4RR5 0 JRNL AUTH Y.LIU,Y.FENG,Y.WANG,X.LI,X.CAO,S.XUE JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF MCAT FROM JRNL TITL 2 PHOTOSYNTHETIC MICROORGANISM SYNECHOCYSTIS SP. PCC 6803 JRNL TITL 3 REVEAL ITS STEPWISE CATALYTIC MECHANISM JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 457 398 2015 JRNL REFN ISSN 0006-291X JRNL PMID 25582772 JRNL DOI 10.1016/J.BBRC.2015.01.003 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 9656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.3505 - 3.5003 0.97 3353 157 0.1564 0.2105 REMARK 3 2 3.5003 - 2.7785 0.91 2968 145 0.2010 0.2847 REMARK 3 3 2.7785 - 2.4273 0.90 2870 163 0.2399 0.3344 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.380 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2245 REMARK 3 ANGLE : 1.114 3046 REMARK 3 CHIRALITY : 0.039 353 REMARK 3 PLANARITY : 0.005 399 REMARK 3 DIHEDRAL : 14.593 814 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4RR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15645 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COOT REMARK 200 STARTING MODEL: 1MLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, 30% PEG 4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 -X+1/2,Y+1/2,-Z 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 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 21.52150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.32300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.52150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.32300 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN A 280 O HOH A 448 1.90 REMARK 500 O ALA A 118 O HOH A 458 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 88 -104.86 57.57 REMARK 500 ALA A 120 53.56 -95.21 REMARK 500 LYS A 130 75.34 61.81 REMARK 500 ALA A 175 138.22 164.38 REMARK 500 ASP A 220 84.99 -159.41 REMARK 500 PRO A 221 31.64 -78.04 REMARK 500 THR A 275 -50.83 -136.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 301 DBREF 4RR5 A 1 293 UNP P73242 FABD_SYNY3 1 293 SEQRES 1 A 293 MET LYS THR ALA TRP VAL PHE PRO GLY GLN GLY SER GLN SEQRES 2 A 293 ALA VAL GLY MET GLY VAL ASP LEU LEU SER THR ALA ILE SEQRES 3 A 293 ALA LYS GLU LYS TYR GLN GLN ALA GLU GLU ILE LEU GLY SEQRES 4 A 293 TRP SER VAL VAL GLU LYS CYS GLN GLY ASP GLU ALA SER SEQRES 5 A 293 LEU ALA LEU THR GLN ASN THR GLN PRO CYS LEU TYR VAL SEQRES 6 A 293 ILE GLU ALA ILE LEU ALA ASP LEU LEU ARG ASP LYS GLY SEQRES 7 A 293 PHE GLN PRO ASP TYR VAL ALA GLY HIS SER LEU GLY GLU SEQRES 8 A 293 TYR SER ALA LEU TYR ALA ALA GLY VAL PHE ASP PHE ALA SEQRES 9 A 293 THR GLY LEU GLN LEU VAL LYS GLN ARG SER GLU VAL MET SEQRES 10 A 293 ALA SER ALA SER GLY GLY MET MET ALA ALA LEU MET LYS SEQRES 11 A 293 PHE ASP GLN THR GLN LEU GLN GLN ALA LEU THR ASP ASN SEQRES 12 A 293 THR GLU VAL VAL LEU ALA ASN ASP ASN SER PRO GLU GLN SEQRES 13 A 293 VAL VAL ILE SER GLY THR VAL ALA GLY VAL GLU ALA ILE SEQRES 14 A 293 LEU ALA ASN VAL LYS ALA ARG ARG ALA VAL PRO LEU LYS SEQRES 15 A 293 VAL SER GLY ALA PHE HIS SER SER PHE MET ALA GLN PRO SEQRES 16 A 293 SER GLN SER PHE ALA GLN THR LEU THR ALA CYS HIS PHE SEQRES 17 A 293 ASN ASP ALA THR VAL PRO VAL LEU SER ASN VAL ASP PRO SEQRES 18 A 293 SER PRO THR GLN ASN GLY ASP ARG LEU LYS GLU LYS LEU SEQRES 19 A 293 ILE GLN GLN MET THR GLY SER VAL ARG TRP ARG GLU THR SEQRES 20 A 293 MET VAL ASN LEU GLY GLU ILE GLY ALA THR ASP TYR TRP SEQRES 21 A 293 GLU VAL GLY PRO GLY LYS VAL LEU THR GLY LEU CYS LYS SEQRES 22 A 293 ARG THR CYS PRO ASP LEU ASN LEU LYS ASN ILE GLY GLN SEQRES 23 A 293 LEU ASP ASP LEU ASN SER LEU HET ACT A 301 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *63(H2 O) HELIX 1 1 GLY A 18 SER A 23 5 6 HELIX 2 2 THR A 24 GLY A 39 1 16 HELIX 3 3 SER A 41 GLN A 47 1 7 HELIX 4 4 ASP A 49 LEU A 55 1 7 HELIX 5 5 LEU A 55 LYS A 77 1 23 HELIX 6 6 LEU A 89 ALA A 98 1 10 HELIX 7 7 ASP A 102 ALA A 120 1 19 HELIX 8 8 ASP A 132 THR A 141 1 10 HELIX 9 9 THR A 162 ASN A 172 1 11 HELIX 10 10 SER A 189 PHE A 191 5 3 HELIX 11 11 MET A 192 ALA A 205 1 14 HELIX 12 12 ASN A 226 GLN A 236 1 11 HELIX 13 13 TRP A 244 GLY A 255 1 12 HELIX 14 14 LYS A 266 ARG A 274 1 9 HELIX 15 15 GLN A 286 SER A 292 1 7 SHEET 1 A 4 TYR A 83 GLY A 86 0 SHEET 2 A 4 THR A 3 PHE A 7 1 N TRP A 5 O TYR A 83 SHEET 3 A 4 ASP A 258 VAL A 262 1 O TRP A 260 N ALA A 4 SHEET 4 A 4 ASN A 280 ILE A 284 1 O ASN A 280 N TYR A 259 SHEET 1 B 5 ALA A 178 PRO A 180 0 SHEET 2 B 5 MET A 124 MET A 129 -1 N ALA A 127 O VAL A 179 SHEET 3 B 5 GLN A 156 GLY A 161 -1 O GLY A 161 N MET A 124 SHEET 4 B 5 VAL A 146 SER A 153 -1 N VAL A 147 O SER A 160 SHEET 5 B 5 VAL A 242 ARG A 243 1 O VAL A 242 N ASP A 151 SHEET 1 C 2 VAL A 215 SER A 217 0 SHEET 2 C 2 ASP A 220 THR A 224 -1 O THR A 224 N VAL A 215 CISPEP 1 ARG A 176 ARG A 177 0 9.40 SITE 1 AC1 6 GLN A 60 SER A 88 ARG A 113 MET A 117 SITE 2 AC1 6 HIS A 188 HOH A 402 CRYST1 43.043 148.646 40.393 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 0.023233 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024757 0.00000