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Yorodumi- PDB-1cl5: CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cl5 | ||||||
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Title | CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA | ||||||
Components | PROTEIN (PHOSPHOLIPASE A2) | ||||||
Keywords | HYDROLASE / PHOSPHOLIPASE A2 / NEUROTOXIC / DABOIA RUSSELLI PULCHELLA | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii pulchella (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Chandra, V. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 A resolution. Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / Singh, T.P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Purification, crystallization and preliminary x-ray crystallographic analysis of a phospholipase A2 from Daboia russelli pulchella. Authors: Chandra, V. / Nagpal, A. / Srinivasan, A. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cl5.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cl5.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cl5 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cl5 | HTTPS FTP |
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-Related structure data
Related structure data | 1pp2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49 % Description: THE R CHAIN OF PDB ENTRY 1PP2 WAS USED FOR MOLECULAR REPLACEMENT. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLISED FROM 1.2 AMMONIUM SULPHATE BUFFER WITH 20MM SODIUM CACODYLATE, 2MM CALCIUM CHLORIDE AND 3% DIOXANE, pH 7.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 47 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 298 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: PIN HOLE |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 61402 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.04 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 16.02 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 14.2 / Rsym value: 0.191 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 10169 / % possible obs: 98 % / Redundancy: 3.9 % |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PP2 Resolution: 2.45→20 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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