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Yorodumi- PDB-4h0s: Crystal structure analysis of a basic phospholipase A2 from Trime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h0s | ||||||
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Title | Crystal structure analysis of a basic phospholipase A2 from Trimeresurus stejnegeri venom | ||||||
Components | Basic phospholipase A2 homolog CTs-R6 | ||||||
Keywords | HYDROLASE / alpha-helix / glycerophospholipid / venom gland | ||||||
Function / homology | Function and homology information phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Viridovipera stejnegeri (Stejneger's pit viper) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Zeng, F. / Niu, L. / Li, X. / Teng, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure analysis of a basic phospholipase A2 from Trimeresurus stejnegeri venom Authors: Zeng, F. / Niu, L. / Li, X. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h0s.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h0s.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 4h0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/4h0s ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h0s | HTTPS FTP |
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-Related structure data
Related structure data | 1b4wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 15322.894 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Viridovipera stejnegeri (Stejneger's pit viper) References: UniProt: Q6H3D7, phospholipase A2 #2: Chemical | ChemComp-NA / #3: 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: 1.94 Å3/Da / Density % sol: 36.69 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2 M sodium chloride, 16% PEG6000, 0.015 mM CYMAL-7, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.97916 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2010 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 51060 / Num. obs: 50982 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5105 / Rsym value: 0.348 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4W Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.548 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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