+Open data
-Basic information
Entry | Database: PDB / ID: 5ptd | ||||||
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Title | PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C MUTANT H32A | ||||||
Components | PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C | ||||||
Keywords | HYDROLASE / PHOSPHORIC DIESTER / LIPID DEGRADATION / PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C | ||||||
Function / homology | Function and homology information phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.7 Å | ||||||
Authors | Heinz, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis. Authors: Gassler, C.S. / Ryan, M. / Liu, T. / Griffith, O.H. / Heinz, D.W. #1: Journal: Embo J. / Year: 1995 Title: Crystal Structure of the Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus in Complex with Myo-Inositol Authors: Heinz, D.W. / Ryan, M. / Bullock, T.L. / Griffith, O.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ptd.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ptd.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ptd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ptd_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 5ptd_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 5ptd_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5ptd_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/5ptd ftp://data.pdbj.org/pub/pdb/validation_reports/pt/5ptd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34501.594 Da / Num. of mol.: 1 / Mutation: H32A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Description: GENE CLONED IN ESCHERICHIA COLI / Cellular location: SECRETED INTO MEDIUM / Gene: PI-PLC GENE / Plasmid: PBR322 RELATED / Cellular location (production host): PERIPLASM / Gene (production host): PI-PLC H32A GENE / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P14262, EC: 3.1.4.10 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 6, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.1 Å / Num. obs: 9252 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.085 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.33 / % possible all: 59.9 |
Reflection | *PLUS Num. measured all: 26905 |
Reflection shell | *PLUS % possible obs: 59.9 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.7→20 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 25.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.271 |