10 20 30 40 50 60 70 80 1PTG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE (PHOSPHORIC DIESTER) 24-MAY-95 1PTG
TITLE PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX TITLE 2 WITH MYO-INOSITOL
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: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 GENE: PI-PLC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBR322 RELATED; SOURCE 8 EXPRESSION_SYSTEM_GENE: PI-PLC
KEYWDS HYDROLASE, PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C, KEYWDS 2 MYO-INOSITOL, INHIBITOR COMPLEX, HYDROLASE (PHOSPHORIC KEYWDS 3 DIESTER)
EXPDTA X-RAY DIFFRACTION
AUTHOR D.W.HEINZ,M.RYAN,T.L.BULLOCK,O.H.GRIFFITH
REVDAT 2 24-FEB-09 1PTG 1 VERSN REVDAT 1 11-JUL-96 1PTG 0
JRNL AUTH D.W.HEINZ,M.RYAN,T.L.BULLOCK,O.H.GRIFFITH JRNL TITL CRYSTAL STRUCTURE OF THE JRNL TITL 2 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM JRNL TITL 3 BACILLUS CEREUS IN COMPLEX WITH MYO-INOSITOL. JRNL REF EMBO J. V. 14 3855 1995 JRNL REFN ISSN 0261-4189 JRNL PMID 7664726
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.L.BULLOCK,M.RYAN,S.L.KIM,S.J.REMINGTON, REMARK 1 AUTH 2 O.H.GRIFFITH REMARK 1 TITL CRYSTALLIZATION OF PHOSPHATIDYLINOSITOL-SPECIFIC REMARK 1 TITL 2 PHOSPHOLIPASE C FROM BACILLUS CEREUS REMARK 1 REF BIOPHYS.J. V. 64 784 1993 REMARK 1 REFN ISSN 0006-3495 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.KUPPE,L.M.EVANS,D.A.MCMILLEN,O.H.GRIFFITH REMARK 1 TITL PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C OF REMARK 1 TITL 2 BACILLUS CEREUS: CLONING, SEQUENCING, AND REMARK 1 TITL 3 RELATIONSHIP TO OTHER PHOSPHOLIPASES REMARK 1 REF J.BACTERIOL. V. 171 6077 1989 REMARK 1 REFN ISSN 0021-9193
REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 77.0 REMARK 3 NUMBER OF REFLECTIONS : 8639 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) : 0.195 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2991 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.50 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) : 0.32 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.46 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 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 1PTG 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 : 1994 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10300 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 22.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.80000 REMARK 290 SMTRY3 4 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 LYS A 297 REMARK 465 GLU A 298
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 PRO A 42 -62.29 -17.29 REMARK 500 VAL A 46 -4.87 -59.34 REMARK 500 TYR A 136 -61.78 -131.14 REMARK 500 TYR A 177 -68.32 -27.15 REMARK 500 VAL A 188 -62.81 -105.20 REMARK 500 ASN A 189 -166.39 -115.41 REMARK 500 ALA A 192 154.33 172.17 REMARK 500 LYS A 201 75.69 60.25 REMARK 500 ASN A 226 55.95 -100.62 REMARK 500 HIS A 227 107.72 -163.40 REMARK 500 THR A 240 -69.68 64.93 REMARK 500 ALA A 241 -161.33 -104.71 REMARK 500 TRP A 242 83.89 -61.87 REMARK 500 ASN A 243 5.16 -170.02 REMARK 500 TYR A 275 69.77 24.58 REMARK 500 ASN A 277 -157.80 -156.93 REMARK 500 TRP A 280 98.28 -59.32 REMARK 500 SER A 281 -52.28 -23.38 REMARK 500 LEU A 283 94.22 65.51 REMARK 500 ALA A 291 0.71 -61.96 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 INS A 801
DBREF 1PTG A 1 298 UNP P14262 PLC_BACCE 32 329
SEQRES 1 A 298 ALA SER SER VAL ASN GLU LEU GLU ASN TRP SER LYS TRP SEQRES 2 A 298 MET GLN PRO ILE PRO ASP SER ILE PRO LEU ALA ARG ILE SEQRES 3 A 298 SER ILE PRO GLY THR HIS ASP SER GLY THR PHE LYS LEU SEQRES 4 A 298 GLN ASN PRO ILE LYS GLN VAL TRP GLY MET THR GLN GLU SEQRES 5 A 298 TYR ASP PHE ARG TYR GLN MET ASP HIS GLY ALA ARG ILE SEQRES 6 A 298 PHE ASP ILE ARG GLY ARG LEU THR ASP ASP ASN THR ILE SEQRES 7 A 298 VAL LEU HIS HIS GLY PRO LEU TYR LEU TYR VAL THR LEU SEQRES 8 A 298 HIS GLU PHE ILE ASN GLU ALA LYS GLN PHE LEU LYS ASP SEQRES 9 A 298 ASN PRO SER GLU THR ILE ILE MET SER LEU LYS LYS GLU SEQRES 10 A 298 TYR GLU ASP MET LYS GLY ALA GLU ASP SER PHE SER SER SEQRES 11 A 298 THR PHE GLU LYS LYS TYR PHE VAL ASP PRO ILE PHE LEU SEQRES 12 A 298 LYS THR GLU GLY ASN ILE LYS LEU GLY ASP ALA ARG GLY SEQRES 13 A 298 LYS ILE VAL LEU LEU LYS ARG TYR SER GLY SER ASN GLU SEQRES 14 A 298 PRO GLY GLY TYR ASN ASN PHE TYR TRP PRO ASP ASN GLU SEQRES 15 A 298 THR PHE THR THR THR VAL ASN GLN ASN ALA ASN VAL THR SEQRES 16 A 298 VAL GLN ASP LYS TYR LYS VAL SER TYR ASP GLU LYS VAL SEQRES 17 A 298 LYS SER ILE LYS ASP THR MET ASP GLU THR MET ASN ASN SEQRES 18 A 298 SER GLU ASP LEU ASN HIS LEU TYR ILE ASN PHE THR SER SEQRES 19 A 298 LEU SER SER GLY GLY THR ALA TRP ASN SER PRO TYR TYR SEQRES 20 A 298 TYR ALA SER TYR ILE ASN PRO GLU ILE ALA ASN TYR ILE SEQRES 21 A 298 LYS GLN LYS ASN PRO ALA ARG VAL GLY TRP VAL ILE GLN SEQRES 22 A 298 ASP TYR ILE ASN GLU LYS TRP SER PRO LEU LEU TYR GLN SEQRES 23 A 298 GLU VAL ILE ARG ALA ASN LYS SER LEU ILE LYS GLU
HET INS A 801 12
HETNAM INS 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
HETSYN INS MYO-INOSITOL
FORMUL 2 INS C6 H12 O6 FORMUL 3 HOH *53(H2 O)
HELIX 1 1 VAL A 4 GLU A 8 5 5 HELIX 2 2 PRO A 42 GLN A 45 1 4 HELIX 3 3 PHE A 55 HIS A 61 1 7 HELIX 4 4 LEU A 91 ASP A 104 1 14 HELIX 5 5 PHE A 128 LYS A 135 1 8 HELIX 6 6 LEU A 151 ALA A 154 1 4 HELIX 7 7 TYR A 204 GLU A 223 1 20 HELIX 8 8 PRO A 245 LYS A 263 1 19 HELIX 9 9 LEU A 284 ASN A 292 1 9
SHEET 1 A 5 ILE A 28 THR A 31 0 SHEET 2 A 5 TRP A 270 GLN A 273 1 N VAL A 271 O ILE A 28 SHEET 3 A 5 LEU A 228 PHE A 232 1 N ASN A 231 O TRP A 270 SHEET 4 A 5 ASN A 193 ASP A 198 1 N THR A 195 O LEU A 228 SHEET 5 A 5 GLU A 182 THR A 187 -1 N THR A 186 O VAL A 194 SHEET 1 B 4 ILE A 78 LEU A 80 0 SHEET 2 B 4 ILE A 65 LEU A 72 -1 N ARG A 71 O VAL A 79 SHEET 3 B 4 ILE A 110 LYS A 116 1 N ILE A 111 O PHE A 66 SHEET 4 B 4 ILE A 158 ARG A 163 1 N VAL A 159 O ILE A 110
SITE 1 AC1 5 HIS A 32 ARG A 69 LYS A 115 ARG A 163 SITE 2 AC1 5 ASP A 198
CRYST1 45.200 45.600 160.800 90.00 90.00 90.00 P 21 21 21 4
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 0.022124 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021930 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006219 0.00000