HEADER TRANSFERASE 19-JUN-07 2QC3 TITLE CRYSTAL STRUCTURE OF MCAT FROM MYCOBACTERIUM TUBERCULOSIS 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: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: FABD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MALONYL-COA:ACP TRANSACYLASE; CRYSTAL STRUCTURE; NUCLEOPHILIC ATTACK; KEYWDS 2 FATTY ACIDS BIOSYNTHESIS; MYCOBACTERIUM TUBERCULOSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI,Y.HUANG,J.GE,M.BARTLAM,H.WANG,Z.RAO REVDAT 5 30-AUG-23 2QC3 1 REMARK SEQADV REVDAT 4 13-JUL-11 2QC3 1 VERSN REVDAT 3 17-NOV-09 2QC3 1 TITLE REVDAT 2 24-FEB-09 2QC3 1 VERSN REVDAT 1 28-AUG-07 2QC3 0 JRNL AUTH Z.LI,Y.HUANG,J.GE,H.FAN,X.ZHOU,S.LI,M.BARTLAM,H.WANG,Z.RAO JRNL TITL THE CRYSTAL STRUCTURE OF MCAT FROM MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS REVEALS THREE NEW CATALYTIC MODELS. JRNL REF J.MOL.BIOL. V. 371 1075 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17604051 JRNL DOI 10.1016/J.JMB.2007.06.004 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 15224 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) : 0.198 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 741 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 : 2160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 321 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) : 0.62800 REMARK 3 B22 (A**2) : -8.69800 REMARK 3 B33 (A**2) : 8.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.86200 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.160 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: NULL REMARK 4 REMARK 4 2QC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19684 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1NM2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M SODIUM ACETATE, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.08550 REMARK 290 SMTRY3 2 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 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 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 LEU A 302 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 O LEU A 143 O HOH A 672 2.15 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 ALA A 48 150.18 -44.93 REMARK 500 SER A 91 -118.48 56.52 REMARK 500 LYS A 181 -8.90 71.91 REMARK 500 ASP A 226 17.18 -149.11 REMARK 500 THR A 261 58.55 -96.38 REMARK 500 ALA A 271 133.17 -39.75 REMARK 500 LEU A 282 66.20 -104.38 REMARK 500 LEU A 296 7.87 -66.04 REMARK 500 ASP A 297 -62.08 -95.96 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 ACY A 500 DBREF 2QC3 A 1 302 UNP P63458 FABD_MYCTU 1 302 SEQADV 2QC3 HIS A 0 UNP P63458 EXPRESSION TAG SEQRES 1 A 303 HIS MET ILE ALA LEU LEU ALA PRO GLY GLN GLY SER GLN SEQRES 2 A 303 THR GLU GLY MET LEU SER PRO TRP LEU GLN LEU PRO GLY SEQRES 3 A 303 ALA ALA ASP GLN ILE ALA ALA TRP SER LYS ALA ALA ASP SEQRES 4 A 303 LEU ASP LEU ALA ARG LEU GLY THR THR ALA SER THR GLU SEQRES 5 A 303 GLU ILE THR ASP THR ALA VAL ALA GLN PRO LEU ILE VAL SEQRES 6 A 303 ALA ALA THR LEU LEU ALA HIS GLN GLU LEU ALA ARG ARG SEQRES 7 A 303 CYS VAL LEU ALA GLY LYS ASP VAL ILE VAL ALA GLY HIS SEQRES 8 A 303 SER VAL GLY GLU ILE ALA ALA TYR ALA ILE ALA GLY VAL SEQRES 9 A 303 ILE ALA ALA ASP ASP ALA VAL ALA LEU ALA ALA THR ARG SEQRES 10 A 303 GLY ALA GLU MET ALA LYS ALA CYS ALA THR GLU PRO THR SEQRES 11 A 303 GLY MET SER ALA VAL LEU GLY GLY ASP GLU THR GLU VAL SEQRES 12 A 303 LEU SER ARG LEU GLU GLN LEU ASP LEU VAL PRO ALA ASN SEQRES 13 A 303 ARG ASN ALA ALA GLY GLN ILE VAL ALA ALA GLY ARG LEU SEQRES 14 A 303 THR ALA LEU GLU LYS LEU ALA GLU ASP PRO PRO ALA LYS SEQRES 15 A 303 ALA ARG VAL ARG ALA LEU GLY VAL ALA GLY ALA PHE HIS SEQRES 16 A 303 THR GLU PHE MET ALA PRO ALA LEU ASP GLY PHE ALA ALA SEQRES 17 A 303 ALA ALA ALA ASN ILE ALA THR ALA ASP PRO THR ALA THR SEQRES 18 A 303 LEU LEU SER ASN ARG ASP GLY LYS PRO VAL THR SER ALA SEQRES 19 A 303 ALA ALA ALA MET ASP THR LEU VAL SER GLN LEU THR GLN SEQRES 20 A 303 PRO VAL ARG TRP ASP LEU CYS THR ALA THR LEU ARG GLU SEQRES 21 A 303 HIS THR VAL THR ALA ILE VAL GLU PHE PRO PRO ALA GLY SEQRES 22 A 303 THR LEU SER GLY ILE ALA LYS ARG GLU LEU ARG GLY VAL SEQRES 23 A 303 PRO ALA ARG ALA VAL LYS SER PRO ALA ASP LEU ASP GLU SEQRES 24 A 303 LEU ALA ASN LEU HET ACY A 500 4 HETNAM ACY ACETIC ACID FORMUL 2 ACY C2 H4 O2 FORMUL 3 HOH *321(H2 O) HELIX 1 1 GLY A 25 ALA A 37 1 13 HELIX 2 2 ASP A 40 THR A 47 1 8 HELIX 3 3 SER A 49 THR A 54 1 6 HELIX 4 4 ASP A 55 ARG A 77 1 23 HELIX 5 5 VAL A 92 ALA A 101 1 10 HELIX 6 6 ALA A 105 ALA A 125 1 21 HELIX 7 7 ASP A 138 LEU A 149 1 12 HELIX 8 8 LEU A 168 ASP A 177 1 10 HELIX 9 9 THR A 195 PRO A 200 5 6 HELIX 10 10 ALA A 201 ASN A 211 1 11 HELIX 11 11 SER A 232 GLN A 243 1 12 HELIX 12 12 LEU A 244 GLN A 246 5 3 HELIX 13 13 TRP A 250 HIS A 260 1 11 HELIX 14 14 THR A 273 LEU A 282 1 10 HELIX 15 15 SER A 292 LEU A 296 5 5 SHEET 1 A 5 THR A 220 LEU A 221 0 SHEET 2 A 5 VAL A 85 GLY A 89 1 N VAL A 87 O THR A 220 SHEET 3 A 5 MET A 1 ALA A 6 1 N LEU A 4 O ILE A 86 SHEET 4 A 5 VAL A 262 GLU A 267 1 O VAL A 266 N ALA A 3 SHEET 5 A 5 ALA A 287 ALA A 289 1 O ARG A 288 N GLU A 267 SHEET 1 B 5 ARG A 183 ALA A 186 0 SHEET 2 B 5 THR A 129 LEU A 135 -1 N LEU A 135 O ARG A 183 SHEET 3 B 5 GLN A 161 ARG A 167 -1 O ALA A 164 N SER A 132 SHEET 4 B 5 VAL A 152 ALA A 158 -1 N VAL A 152 O ALA A 165 SHEET 5 B 5 VAL A 248 ARG A 249 1 O VAL A 248 N ALA A 154 CISPEP 1 PRO A 269 PRO A 270 0 -0.27 SITE 1 AC1 6 GLN A 9 SER A 91 VAL A 92 ARG A 116 SITE 2 AC1 6 PHE A 193 HIS A 194 CRYST1 36.520 48.171 77.414 90.00 98.89 90.00 P 1 21 1 2 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 0.027382 0.000000 0.004283 0.00000 SCALE2 0.000000 0.020759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013075 0.00000