HEADER HYDROLASE 09-JUL-97 2PLC TITLE PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM LISTERIA TITLE 2 MONOCYTOGENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PI-PLC; COMPND 5 EC: 3.1.4.10; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 3 ORGANISM_TAXID: 1639; SOURCE 4 STRAIN: EGD SEROTYPE 1-2A; SOURCE 5 CELL_LINE: BL21; SOURCE 6 CELLULAR_LOCATION: SECRETED INTO MEDIUM; SOURCE 7 GENE: PLCA; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PLCA; SOURCE 14 EXPRESSION_SYSTEM_GENE: PLCA DELETION VARIANT KEYWDS HYDROLASE, PHOSPHOLIPID DEGRADATION, VIRULENCE FACTOR OF KEYWDS 2 HUMAN PATHOGEN EXPDTA X-RAY DIFFRACTION AUTHOR D.W.HEINZ,J.MOSER REVDAT 2 24-FEB-09 2PLC 1 VERSN REVDAT 1 14-JAN-98 2PLC 0 JRNL AUTH J.MOSER,B.GERSTEL,J.E.MEYER,T.CHAKRABORTY, JRNL AUTH 2 J.WEHLAND,D.W.HEINZ JRNL TITL CRYSTAL STRUCTURE OF THE JRNL TITL 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM JRNL TITL 3 THE HUMAN PATHOGEN LISTERIA MONOCYTOGENES. JRNL REF J.MOL.BIOL. V. 273 269 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9367761 JRNL DOI 10.1006/JMBI.1997.1290 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 23003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1164 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2191 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.19 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2208 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : NULL REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.08 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUPED B-FACTOR REFINEME 2 REMARK 3 PARAMETERS PER RESIDUE 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 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : -P19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 7 - 20 WERE MISSING IN THE REMARK 3 ELECTRON DENSITY MAP. THESE RESIDUES WERE IDENTIFIED VIA N- REMARK 3 TERMINAL SEQUENCING. REMARK 4 REMARK 4 2PLC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI-FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25523 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : 0.20200 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 AND SIG REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: PDB ENTRY 1PTD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 0.1 M REMARK 280 NA-HEPES PH 7.5, 0.8 M NA-K-TARTRATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 30.73333 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 61.46667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.46667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.73333 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 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 GLN A 25 42.43 -141.62 REMARK 500 ASP A 87 -8.14 -58.64 REMARK 500 GLN A 129 54.94 -140.08 REMARK 500 ASN A 130 103.96 -49.04 REMARK 500 SER A 131 -3.30 -178.03 REMARK 500 ASN A 160 43.30 33.49 REMARK 500 ASN A 187 -116.92 73.09 REMARK 500 ASN A 207 82.89 -66.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 333 DISTANCE = 9.51 ANGSTROMS REMARK 525 HOH A 361 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A 374 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 376 DISTANCE = 10.46 ANGSTROMS REMARK 525 HOH A 387 DISTANCE = 5.32 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CIC REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: INOSITOL BINDING SITE. DBREF 2PLC A 21 294 UNP P34024 PLC_LISMO 43 316 SEQRES 1 A 274 VAL THR THR LYS GLN TRP MET SER ALA LEU PRO ASP THR SEQRES 2 A 274 THR ASN LEU ALA ALA LEU SER ILE PRO GLY THR HIS ASP SEQRES 3 A 274 THR MET SER TYR ASN GLY ASP ILE THR TRP THR LEU THR SEQRES 4 A 274 LYS PRO LEU ALA GLN THR GLN THR MET SER LEU TYR GLN SEQRES 5 A 274 GLN LEU GLU ALA GLY ILE ARG TYR ILE ASP ILE ARG ALA SEQRES 6 A 274 LYS ASP ASN LEU ASN ILE TYR HIS GLY PRO ILE PHE LEU SEQRES 7 A 274 ASN ALA SER LEU SER GLY VAL LEU GLU THR ILE THR GLN SEQRES 8 A 274 PHE LEU LYS LYS ASN PRO LYS GLU THR ILE ILE MET ARG SEQRES 9 A 274 LEU LYS ASP GLU GLN ASN SER ASN ASP SER PHE ASP TYR SEQRES 10 A 274 ARG ILE GLN PRO LEU ILE ASN ILE TYR LYS ASP TYR PHE SEQRES 11 A 274 TYR THR THR PRO ARG THR ASP THR SER ASN LYS ILE PRO SEQRES 12 A 274 THR LEU LYS ASP VAL ARG GLY LYS ILE LEU LEU LEU SER SEQRES 13 A 274 GLU ASN HIS THR LYS LYS PRO LEU VAL ILE ASN SER ARG SEQRES 14 A 274 LYS PHE GLY MET GLN PHE GLY ALA PRO ASN GLN VAL ILE SEQRES 15 A 274 GLN ASP ASP TYR ASN GLY PRO SER VAL LYS THR LYS PHE SEQRES 16 A 274 LYS GLU ILE VAL GLN THR ALA TYR GLN ALA SER LYS ALA SEQRES 17 A 274 ASP ASN LYS LEU PHE LEU ASN HIS ILE SER ALA THR SER SEQRES 18 A 274 LEU THR PHE THR PRO ARG GLN TYR ALA ALA ALA LEU ASN SEQRES 19 A 274 ASN LYS VAL GLU GLN PHE VAL LEU ASN LEU THR SER GLU SEQRES 20 A 274 LYS VAL ARG GLY LEU GLY ILE LEU ILE MET ASP PHE PRO SEQRES 21 A 274 GLU LYS GLN THR ILE LYS ASN ILE ILE LYS ASN ASN LYS SEQRES 22 A 274 PHE FORMUL 2 HOH *102(H2 O) HELIX 1 1 GLN A 25 ALA A 29 5 5 HELIX 2 2 ILE A 54 PRO A 61 1 8 HELIX 3 3 LEU A 70 GLY A 77 1 8 HELIX 4 4 SER A 103 ASN A 116 1 14 HELIX 5 5 PHE A 135 ILE A 145 1 11 HELIX 6 6 VAL A 211 ALA A 228 1 18 HELIX 7 7 THR A 245 LYS A 268 1 24 HELIX 8 8 GLU A 281 ILE A 289 1 9 SHEET 1 A 4 SER A 40 ASP A 46 0 SHEET 2 A 4 GLY A 273 ASP A 278 1 N GLY A 273 O ILE A 41 SHEET 3 A 4 LEU A 232 ILE A 237 1 N ASN A 235 O ILE A 274 SHEET 4 A 4 VAL A 201 TYR A 206 1 N VAL A 201 O LEU A 232 SHEET 1 B 3 ARG A 79 LYS A 86 0 SHEET 2 B 3 ILE A 121 GLU A 128 1 N ILE A 122 O ILE A 81 SHEET 3 B 3 LYS A 171 ASN A 178 1 N LEU A 173 O ILE A 121 SHEET 1 C 3 TYR A 151 THR A 156 0 SHEET 2 C 3 PHE A 191 GLY A 196 1 SHEET 3 C 3 VAL A 185 ILE A 186 -1 SITE 1 CIC 2 HIS A 45 HIS A 93 CRYST1 82.500 82.500 92.200 90.00 90.00 120.00 P 31 2 1 6 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 0.012121 0.006998 0.000000 0.00000 SCALE2 0.000000 0.013996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010846 0.00000 MASTER 262 0 0 8 10 0 1 6 0 0 0 22 END