HEADER TRANSFERASE 28-APR-09 3H7Q TITLE CRYSTAL STRUCTURE OF THE HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE (ACPS) TITLE 2 FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 4'-PHOSPHOPANTETHEINYL TRANSFERASE ACPS, HOLO-ACP SYNTHASE; COMPND 5 EC: 2.7.8.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV2523C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS HOMO-TRIMER, 9-STAND PSEUDO BETA BARREL PROTEIN, CYTOPLASM, FATTY KEYWDS 2 ACID BIOSYNTHESIS, LIPID SYNTHESIS, MAGNESIUM, METAL-BINDING, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.POULSEN,M.WILMANNS,Y.H.SONG REVDAT 2 01-NOV-23 3H7Q 1 REMARK SEQADV REVDAT 1 07-APR-10 3H7Q 0 JRNL AUTH C.POULSEN,M.WILMANNS,Y.H.SONG JRNL TITL STRUCTURE OF THE HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE (ACPS) JRNL TITL 2 FROM MYCOBACTERIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 359 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 24.5690 - 3.2440 0.98 2250 119 0.2020 0.2320 REMARK 3 2 3.2440 - 2.5760 0.99 2282 120 0.1920 0.2740 REMARK 3 3 2.5760 - 2.2500 0.99 2283 120 0.2370 0.2820 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 : 0.28 REMARK 3 B_SOL : 53.27 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.55000 REMARK 3 B22 (A**2) : 4.55000 REMARK 3 B33 (A**2) : -9.10100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 901 REMARK 3 ANGLE : 0.787 1224 REMARK 3 CHIRALITY : 0.051 145 REMARK 3 PLANARITY : 0.004 160 REMARK 3 DIHEDRAL : 15.405 313 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 3H7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7176 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06400 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) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GWM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90MM BICINE PH 9.0, 17%(V/V) PEG MME REMARK 280 550, 15%(V/V) GLYCEROL, 90MM NACL, VAPOR DIFFUSION, TEMPERATURE REMARK 280 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.40500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.86374 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.94667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 34.40500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 19.86374 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.94667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 34.40500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 19.86374 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.94667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.72747 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.89333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 39.72747 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.89333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 39.72747 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.89333 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GLN A 71 REMARK 465 ARG A 72 REMARK 465 PRO A 73 REMARK 465 VAL A 74 REMARK 465 LEU A 75 REMARK 465 PRO A 76 REMARK 465 GLU A 77 REMARK 465 ASP A 78 REMARK 465 ASP A 88 REMARK 465 MET A 89 REMARK 465 TRP A 90 REMARK 465 GLY A 91 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 79 CG1 CG2 CD1 REMARK 470 HIS A 80 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCN A 131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GWM RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM MYCOBACTERIUM SMEGMATIS DBREF 3H7Q A 1 130 UNP P0A4W8 ACPS_MYCTU 1 130 SEQADV 3H7Q GLY A -1 UNP P0A4W8 EXPRESSION TAG SEQADV 3H7Q ALA A 0 UNP P0A4W8 EXPRESSION TAG SEQRES 1 A 132 GLY ALA MET GLY ILE VAL GLY VAL GLY ILE ASP LEU VAL SEQRES 2 A 132 SER ILE PRO ASP PHE ALA GLU GLN VAL ASP GLN PRO GLY SEQRES 3 A 132 THR VAL PHE ALA GLU THR PHE THR PRO GLY GLU ARG ARG SEQRES 4 A 132 ASP ALA SER ASP LYS SER SER SER ALA ALA ARG HIS LEU SEQRES 5 A 132 ALA ALA ARG TRP ALA ALA LYS GLU ALA VAL ILE LYS ALA SEQRES 6 A 132 TRP SER GLY SER ARG PHE ALA GLN ARG PRO VAL LEU PRO SEQRES 7 A 132 GLU ASP ILE HIS ARG ASP ILE GLU VAL VAL THR ASP MET SEQRES 8 A 132 TRP GLY ARG PRO ARG VAL ARG LEU THR GLY ALA ILE ALA SEQRES 9 A 132 GLU TYR LEU ALA ASP VAL THR ILE HIS VAL SER LEU THR SEQRES 10 A 132 HIS GLU GLY ASP THR ALA ALA ALA VAL ALA ILE LEU GLU SEQRES 11 A 132 ALA PRO HET BCN A 131 11 HETNAM BCN BICINE FORMUL 2 BCN C6 H13 N O4 FORMUL 3 HOH *47(H2 O) HELIX 1 1 ILE A 13 ASP A 21 1 9 HELIX 2 2 THR A 25 PHE A 31 1 7 HELIX 3 3 THR A 32 SER A 40 1 9 HELIX 4 4 SER A 44 GLY A 66 1 23 HELIX 5 5 THR A 98 LEU A 105 1 8 SHEET 1 A 3 GLY A 2 SER A 12 0 SHEET 2 A 3 THR A 120 ALA A 129 -1 O LEU A 127 N VAL A 4 SHEET 3 A 3 THR A 109 GLU A 117 -1 N GLU A 117 O THR A 120 SHEET 1 B 2 ILE A 83 VAL A 86 0 SHEET 2 B 2 ARG A 94 LEU A 97 -1 O ARG A 94 N VAL A 86 SITE 1 AC1 5 ASP A 9 LEU A 10 LYS A 62 THR A 115 SITE 2 AC1 5 HIS A 116 CRYST1 68.810 68.810 86.840 90.00 90.00 120.00 H 3 9 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 0.014533 0.008390 0.000000 0.00000 SCALE2 0.000000 0.016781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011515 0.00000