+Open data
-Basic information
Entry | Database: PDB / ID: 1ah7 | ||||||
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Title | PHOSPHOLIPASE C FROM BACILLUS CEREUS | ||||||
Components | PHOSPHOLIPASE C | ||||||
Keywords | HYDROLASE / LIPASE / PHOSPHOLIPID HYDROLYSIS | ||||||
Function / homology | Function and homology information phospholipase C / phosphatidylcholine phospholipase C activity / killing of cells of another organism / zinc ion binding Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.501 Å | ||||||
Authors | Greaves, R. | ||||||
Citation | Journal: Nature / Year: 1989 Title: High-resolution (1.5 A) crystal structure of phospholipase C from Bacillus cereus. Authors: Hough, E. / Hansen, L.K. / Birknes, B. / Jynge, K. / Hansen, S. / Hordvik, A. / Little, C. / Dodson, E. / Derewenda, Z. #1: Journal: Lipases : Their Structure, Biochemistry, and Application Year: 1994 Title: Structural Aspects of Phospholipase C from Bacillus Cereus and its Reaction Mechanism Authors: Hough, E. / Hansen, S. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystal Structure of Phospholipase C from Bacillus Cereus Complexed with a Substrate Analog Authors: Hansen, S. / Hough, E. / Svensson, L.A. / Wong, Y.L. / Martin, S.F. #3: Journal: J.Mol.Biol. / Year: 1993 Title: The Crystal Structure of Tris-Inhibited Phospholipase C from Bacillus Cereus at 1.9 A Resolution. The Nature of the Metal Ion in Site 2 Authors: Hansen, S. / Hansen, L.K. / Hough, E. #4: Journal: J.Mol.Biol. / Year: 1992 Title: Crystal Structures of Phosphate, Iodide and Iodate-Inhibited Phospholipase C from Bacillus Cereus and Structural Investigations of the Binding of Reaction Products and a Substrate Analogue Authors: Hansen, S. / Hansen, L.K. / Hough, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ah7.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ah7.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1ah7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/1ah7 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/1ah7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28423.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus cereus (bacteria) / References: UniProt: P09598, phospholipase C | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.7 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 Details: VAPOR PHASE DIFFUSION FROM SOLUTION OF 5MG/ML PLC IN 35% SATURATED AMMONIUM SULFATE, pH 7, vapor diffusion | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 1, 1986 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→12.45 Å / Num. obs: 46061 / % possible obs: 95 % / Redundancy: 2.5 % / Rsym value: 0.056 |
Reflection shell | Resolution: 1.501→1.57 Å / % possible all: 82 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.501→12.451 Å / Cross valid method: FREE R / σ(F): 0 Details: PROTEIN MODEL DID NOT INCLUDE HYDROGEN ATOM POSITIONS. INITIAL REFINEMENT WAS PERFORMED USING USING PROTIN AND PROLSQ. THERE IS STILL SOME DOUBT ABOUT THE EXACT POSITIONING OF TYR 156 WHICH ...Details: PROTEIN MODEL DID NOT INCLUDE HYDROGEN ATOM POSITIONS. INITIAL REFINEMENT WAS PERFORMED USING USING PROTIN AND PROLSQ. THERE IS STILL SOME DOUBT ABOUT THE EXACT POSITIONING OF TYR 156 WHICH IS NOT WITHIN THE EXPECTED DISTRIBUTION OF RING PLANARITY FOR TYROSINE RESIDUES. THE DENSITY AROUND THE C-TERMINUS WAS POOR. THE POSITIONING OF RESIDUES ASP 244 AND ARG 245 IS THUS AMBIGUOUS.
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Refinement step | Cycle: LAST / Resolution: 1.501→12.451 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Num. reflection all: 48722 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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