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Yorodumi- PDB-1vip: ANTICOAGULANT CLASS II PHOSPHOLIPASE A2 FROM THE VENOM OF VIPERA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vip | ||||||
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Title | ANTICOAGULANT CLASS II PHOSPHOLIPASE A2 FROM THE VENOM OF VIPERA RUSSELLI RUSSELLI | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / PHOSPHOLIPASE A2 / ANTICOAGULANT | ||||||
Function / homology | Function and homology information phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Daboia russellii russellii (snake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Carredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H. | ||||||
Citation | Journal: Toxicon / Year: 1998 Title: The three-dimensional structures of two toxins from snake venom throw light on the anticoagulant and neurotoxic sites of phospholipase A2. Authors: Carredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vip.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vip.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vip_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 1vip_full_validation.pdf.gz | 417.1 KB | Display | |
Data in XML | 1vip_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1vip_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/1vip ftp://data.pdbj.org/pub/pdb/validation_reports/vi/1vip | HTTPS FTP |
-Related structure data
Related structure data | 2notC 1pp2S 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13644.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIAMI SERPENTARIUM / Source: (natural) Daboia russellii russellii (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: russellii / References: UniProt: P81458, phospholipase A2 |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.81 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.25 Details: PROTEIN WAS CRYSTALLIZED FROM 1.4 M AMSO4,N50 MM AMOAC AND 2 % DIOXANE AT PH 6.25. | ||||||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 8, 1993 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 8258 / % possible obs: 99.2 % / Observed criterion σ(I): 0.001 / Redundancy: 7.2 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.039 / % possible all: 98.5 |
Reflection | *PLUS Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.855 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PP2 Resolution: 2.2→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.042 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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