HEADER LYASE 24-NOV-14 4RV3 TITLE CRYSTAL STRUCTURE OF A PENTAFLUORO-PHE INCORPORATED TITLE 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C (H258X)FROM TITLE 3 STAPHYLOCOCCUS AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-PHOSPHATIDYLINOSITOL PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.6.1.13; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 426430; SOURCE 4 STRAIN: NEWMAN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CATION-PI, TIM BARREL, ENCODED UNNATURAL AMINO ACID PHOSPHOLIPASE, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HE,A.GERSHENSON,S.J.EYLES,J.GAO,M.F.ROBERTS REVDAT 4 29-AUG-18 4RV3 1 COMPND SOURCE REVDAT 3 19-AUG-15 4RV3 1 JRNL REVDAT 2 15-JUL-15 4RV3 1 JRNL REVDAT 1 01-JUL-15 4RV3 0 JRNL AUTH T.HE,A.GERSHENSON,S.J.EYLES,Y.J.LEE,W.R.LIU,J.WANG,J.GAO, JRNL AUTH 2 M.F.ROBERTS JRNL TITL FLUORINATED AROMATIC AMINO ACIDS DISTINGUISH CATION-PI JRNL TITL 2 INTERACTIONS FROM MEMBRANE INSERTION. JRNL REF J.BIOL.CHEM. V. 290 19334 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26092728 JRNL DOI 10.1074/JBC.M115.668343 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 22307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1139 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 49.8867 - 3.9995 0.99 2978 125 0.1488 0.1708 REMARK 3 2 3.9995 - 3.1747 1.00 2775 153 0.1727 0.2263 REMARK 3 3 3.1747 - 2.7734 1.00 2718 167 0.2045 0.2728 REMARK 3 4 2.7734 - 2.5199 1.00 2711 144 0.2106 0.2875 REMARK 3 5 2.5199 - 2.3393 1.00 2718 131 0.2027 0.2821 REMARK 3 6 2.3393 - 2.2013 1.00 2658 166 0.1873 0.2762 REMARK 3 7 2.2013 - 2.0911 0.96 2575 139 0.1985 0.2517 REMARK 3 8 2.0911 - 2.0000 0.77 2035 114 0.2007 0.2872 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.120 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 : 0.007 2507 REMARK 3 ANGLE : 1.020 3394 REMARK 3 CHIRALITY : 0.051 359 REMARK 3 PLANARITY : 0.004 432 REMARK 3 DIHEDRAL : 13.745 906 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 4RV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.6 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC VARIMAX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22311 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 49.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.310 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.13 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 4000,0.150M AMMONIUM REMARK 280 ACETATE,0.1M SODIUM ACETATE, 0.1M MAGNESIUM NITRATE, PH 4.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 90.20500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.92500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.30750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.92500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.92500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.10250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.92500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.92500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 135.30750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.92500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.92500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.10250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.20500 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: 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 TYR A 134 -61.79 -129.55 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE INS A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3V16 RELATED DB: PDB REMARK 900 PI-PLC FROM S. AUREUS DBREF 4RV3 A 2 302 UNP P45723 PLC_STAAE 11 311 SEQADV 4RV3 PF5 A 258 UNP P45723 HIS 267 ENGINEERED MUTATION SEQADV 4RV3 LEU A 303 UNP P45723 EXPRESSION TAG SEQRES 1 A 302 ASP SER LEU SER LYS SER PRO GLU ASN TRP MET SER LYS SEQRES 2 A 302 LEU ASP ASP GLY LYS HIS LEU THR GLU ILE ASN ILE PRO SEQRES 3 A 302 GLY SER HIS ASP SER GLY SER PHE THR LEU LYS ASP PRO SEQRES 4 A 302 VAL LYS SER VAL TRP ALA LYS THR GLN ASP LYS ASP TYR SEQRES 5 A 302 LEU THR GLN MET LYS SER GLY VAL ARG PHE PHE ASP ILE SEQRES 6 A 302 ARG GLY ARG ALA SER ALA ASP ASN MET ILE SER VAL HIS SEQRES 7 A 302 HIS GLY MET VAL TYR LEU HIS HIS GLU LEU GLY LYS PHE SEQRES 8 A 302 LEU ASP ASP ALA LYS TYR TYR LEU SER ALA TYR PRO ASN SEQRES 9 A 302 GLU THR ILE VAL MET SER MET LYS LYS ASP TYR ASP SER SEQRES 10 A 302 ASP SER LYS VAL THR LYS THR PHE GLU GLU ILE PHE ARG SEQRES 11 A 302 GLU TYR TYR TYR ASN ASN PRO GLN TYR GLN ASN LEU PHE SEQRES 12 A 302 TYR THR GLY SER ASN ALA ASN PRO THR LEU LYS GLU THR SEQRES 13 A 302 LYS GLY LYS ILE VAL LEU PHE ASN ARG MET GLY GLY THR SEQRES 14 A 302 TYR ILE LYS SER GLY TYR GLY ALA ASP THR SER GLY ILE SEQRES 15 A 302 GLN TRP ALA ASP ASN ALA THR PHE GLU THR LYS ILE ASN SEQRES 16 A 302 ASN GLY SER LEU ASN LEU LYS VAL GLN ASP GLU TYR LYS SEQRES 17 A 302 ASP TYR TYR ASP LYS LYS VAL GLU ALA VAL LYS ASN LEU SEQRES 18 A 302 LEU ALA LYS ALA LYS THR ASP SER ASN LYS ASP ASN VAL SEQRES 19 A 302 TYR VAL ASN PHE LEU SER VAL ALA SER GLY GLY SER ALA SEQRES 20 A 302 PHE ASN SER THR TYR ASN TYR ALA SER PF5 ILE ASN PRO SEQRES 21 A 302 GLU ILE ALA LYS THR ILE LYS ALA ASN GLY LYS ALA ARG SEQRES 22 A 302 THR GLY TRP LEU ILE VAL ASP TYR ALA GLY TYR THR TRP SEQRES 23 A 302 PRO GLY TYR ASP ASP ILE VAL SER GLU ILE ILE ASP SER SEQRES 24 A 302 ASN LYS LEU MODRES 4RV3 PF5 A 258 PHE 2,3,4,5,6-PENTAFLUORO-L-PHENYLALANINE HET PF5 A 258 16 HET ACT A 401 4 HET INS A 402 12 HETNAM PF5 2,3,4,5,6-PENTAFLUORO-L-PHENYLALANINE HETNAM ACT ACETATE ION HETNAM INS 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE HETSYN PF5 FLUORINATED PHENYLALANINE HETSYN INS MYO-INOSITOL FORMUL 1 PF5 C9 H6 F5 N O2 FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 INS C6 H12 O6 FORMUL 4 HOH *161(H2 O) HELIX 1 1 SER A 3 LEU A 15 5 13 HELIX 2 2 HIS A 20 ILE A 24 5 5 HELIX 3 3 ASP A 31 LEU A 37 5 7 HELIX 4 4 ASP A 39 LYS A 47 1 9 HELIX 5 5 ASP A 52 SER A 59 1 8 HELIX 6 6 LEU A 89 TYR A 103 1 15 HELIX 7 7 THR A 125 TYR A 134 1 10 HELIX 8 8 THR A 153 LYS A 158 1 6 HELIX 9 9 TYR A 211 THR A 228 1 18 HELIX 10 10 SER A 247 ASN A 250 5 4 HELIX 11 11 SER A 251 ALA A 269 1 19 HELIX 12 12 ASP A 292 SER A 300 1 9 SHEET 1 A 5 VAL A 83 GLU A 88 0 SHEET 2 A 5 MET A 75 HIS A 80 -1 N VAL A 78 O HIS A 87 SHEET 3 A 5 PHE A 63 ALA A 72 -1 N ARG A 69 O SER A 77 SHEET 4 A 5 ILE A 108 LYS A 114 1 O SER A 111 N PHE A 64 SHEET 5 A 5 ILE A 161 ARG A 166 1 O VAL A 162 N ILE A 108 SHEET 1 B 8 VAL A 83 GLU A 88 0 SHEET 2 B 8 MET A 75 HIS A 80 -1 N VAL A 78 O HIS A 87 SHEET 3 B 8 PHE A 63 ALA A 72 -1 N ARG A 69 O SER A 77 SHEET 4 B 8 ILE A 26 SER A 29 1 N SER A 29 O PHE A 63 SHEET 5 B 8 TRP A 277 VAL A 280 1 O LEU A 278 N GLY A 28 SHEET 6 B 8 ASN A 234 PHE A 239 1 N ASN A 238 O TRP A 277 SHEET 7 B 8 LEU A 200 ASP A 206 1 N LYS A 203 O VAL A 235 SHEET 8 B 8 ALA A 189 ILE A 195 -1 N PHE A 191 O VAL A 204 LINK C SER A 257 N PF5 A 258 1555 1555 1.33 LINK C PF5 A 258 N ILE A 259 1555 1555 1.34 SITE 1 AC1 5 LEU A 37 LYS A 38 ASP A 39 LYS A 42 SITE 2 AC1 5 HIS A 86 SITE 1 AC2 8 HIS A 30 ARG A 67 LYS A 113 ARG A 166 SITE 2 AC2 8 ASP A 206 HOH A 503 HOH A 546 HOH A 563 CRYST1 59.850 59.850 180.410 90.00 90.00 90.00 P 43 21 2 8 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 0.016708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005543 0.00000 MASTER 244 0 3 12 13 0 4 6 0 0 0 24 END