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Yorodumi- PDB-1aod: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM LISTERIA MONOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aod | ||||||
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Title | PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM LISTERIA MONOCYTOGENES | ||||||
Components | PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE CPhosphoinositide phospholipase C | ||||||
Keywords | HYDROLASE / PHOSPHOLIPID DEGRADATION / VIRULENCE FACTOR OF HUMAN PATHOGEN | ||||||
Function / homology | Function and homology information phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Heinz, D.W. / Moser, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes. Authors: Moser, J. / Gerstel, B. / Meyer, J.E. / Chakraborty, T. / Wehland, J. / Heinz, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aod.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aod.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 1aod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/1aod ftp://data.pdbj.org/pub/pdb/validation_reports/ao/1aod | HTTPS FTP |
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-Related structure data
Related structure data | 2plcC 1ptdS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 32972.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BOUND MYO-INOSITOL IN ACTIVE SITE / Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD SEROTYPE 1/2A / Cell line: BL21 / Cellular location: SECRETED INTO MEDIUM / Gene: PLCA / Plasmid: PLCA / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): PLCA DELETION VARIANT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P34024, EC: 3.1.4.10 |
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#2: Chemical | ChemComp-INS / |
#3: 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: 2.7 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.1 M NA-HEPES PH 7.5, 0.8 M NA-K-TARTRATE, 45 MM MYO-INOSITOL | |||||||||||||||||||||||||
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 | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 1996 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→24 Å / Num. obs: 10914 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.104 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.41 / % possible all: 97 |
Reflection | *PLUS % possible obs: 95.3 % / Num. measured all: 43095 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PTD Resolution: 2.6→20 Å / Rfactor Rfree error: 0.0065 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 Isotropic thermal model: GROUPED B-FACTOR REFINEME 2 PARAMETERS PER RESIDUE Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.241 |