HEADER TRANSFERASE 01-APR-09 3GWM TITLE CRYSTAL STRUCTURE OF THE HOLO-[ACYL-CARRIER-PROTEIN] SYNTHASE (ACPS) TITLE 2 FROM MYCOBACTERIUM SMEGMATIS 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155 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 3 20-MAR-24 3GWM 1 REMARK REVDAT 2 01-NOV-17 3GWM 1 REMARK REVDAT 1 07-APR-10 3GWM 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 15958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 798 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 21.8530 - 3.0800 0.99 2539 133 0.1580 0.1710 REMARK 3 2 3.0800 - 2.4460 0.99 2540 134 0.1500 0.1990 REMARK 3 3 2.4460 - 2.1370 0.99 2541 134 0.1690 0.1850 REMARK 3 4 2.1370 - 1.9420 1.00 2537 133 0.1750 0.2150 REMARK 3 5 1.9420 - 1.8030 0.99 2561 135 0.2270 0.2890 REMARK 3 6 1.8030 - 1.6960 0.95 2442 129 0.2400 0.2890 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 : 0.44 REMARK 3 B_SOL : 56.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.41200 REMARK 3 B22 (A**2) : 1.41200 REMARK 3 B33 (A**2) : -2.82400 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 : 0.005 2021 REMARK 3 ANGLE : 0.743 3663 REMARK 3 CHIRALITY : 0.063 158 REMARK 3 PLANARITY : 0.003 306 REMARK 3 DIHEDRAL : 13.132 502 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 3GWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04700 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PH 6.5, 16% PEG 400, REMARK 280 200MM (NH4)SO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 33.72500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.47114 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.68667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 33.72500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 19.47114 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.68667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 33.72500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 19.47114 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.68667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.94228 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 57.37333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 38.94228 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 57.37333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 38.94228 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 57.37333 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: 5740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 150 LIES ON A SPECIAL POSITION. 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 MET A 89 1.28 -69.54 REMARK 500 ASP A 118 -118.55 55.35 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 SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 132 DBREF 3GWM A 2 130 UNP A0R1H6 ACPS_MYCS2 2 130 SEQRES 1 A 129 ALA ILE VAL GLY VAL GLY ILE ASP LEU VAL SER ILE PRO SEQRES 2 A 129 ASP PHE ALA GLU GLN VAL ASP ARG PRO GLY THR VAL PHE SEQRES 3 A 129 ALA GLU THR PHE THR PRO GLY GLU ARG ARG ASP ALA ALA SEQRES 4 A 129 ASP LYS SER SER SER ALA ALA ARG HIS LEU ALA ALA ARG SEQRES 5 A 129 TRP ALA ALA LYS GLU ALA VAL ILE LYS ALA TRP SER SER SEQRES 6 A 129 SER ARG PHE SER LYS ARG PRO ALA LEU PRO GLU GLY ILE SEQRES 7 A 129 HIS ARG ASP ILE GLU VAL VAL THR ASP MET TRP GLY ARG SEQRES 8 A 129 PRO LYS VAL ARG LEU SER GLY GLU ILE ALA LYS HIS LEU SEQRES 9 A 129 GLU ASP VAL THR ILE HIS VAL SER LEU THR HIS GLU ASP SEQRES 10 A 129 GLN THR ALA ALA ALA VAL ALA ILE ILE GLU GLU PRO HET SO4 A 1 5 HET SO4 A 131 5 HET SO4 A 132 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *155(H2 O) HELIX 1 1 ILE A 13 ASP A 21 1 9 HELIX 2 2 GLY A 24 GLU A 29 1 6 HELIX 3 3 THR A 32 ALA A 40 1 9 HELIX 4 4 SER A 44 SER A 66 1 23 HELIX 5 5 GLY A 78 ASP A 82 1 5 HELIX 6 6 SER A 98 LEU A 105 1 8 SHEET 1 A 3 ILE A 3 SER A 12 0 SHEET 2 A 3 THR A 120 GLU A 128 -1 O ILE A 127 N VAL A 4 SHEET 3 A 3 THR A 109 GLU A 117 -1 N THR A 109 O GLU A 128 SHEET 1 B 2 ILE A 83 THR A 87 0 SHEET 2 B 2 PRO A 93 LEU A 97 -1 O LYS A 94 N VAL A 86 SITE 1 AC1 10 ASP A 9 LYS A 62 LEU A 114 THR A 115 SITE 2 AC1 10 HIS A 116 HOH A 139 HOH A 154 HOH A 192 SITE 3 AC1 10 HOH A 242 HOH A 247 SITE 1 AC2 7 GLU A 29 GLU A 77 GLY A 78 ILE A 79 SITE 2 AC2 7 HIS A 80 ARG A 81 HOH A 214 SITE 1 AC3 5 ARG A 48 HIS A 49 HIS A 116 HOH A 143 SITE 2 AC3 5 HOH A 283 CRYST1 67.450 67.450 86.060 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 0.014826 0.008560 0.000000 0.00000 SCALE2 0.000000 0.017119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011620 0.00000