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Yorodumi- PDB-2ph4: Crystal structure of a novel Arg49 phospholipase A2 homologue fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ph4 | ||||||
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Title | Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom | ||||||
Components | Zhaoermiatoxin | ||||||
Keywords | TOXIN / snake venom / arg49 / phospholipase A2 / myotoxin | ||||||
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 | Zhaoermia mangshanensis (snake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Murakami, M.T. / Kuch, U. / Mebs, D. / Arni, R.K. | ||||||
Citation | Journal: Toxicon / Year: 2008 Title: Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the ...Title: Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus. Authors: Murakami, M.T. / Kuch, U. / Betzel, C. / Mebs, D. / Arni, R.K. | ||||||
History |
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Remark 999 | sequence THE SEQUENCE IS NUMBERED BASED ON THE BOVINE PANCREATIC PHOSPHOLIPASE A2. SO, NOT ...sequence THE SEQUENCE IS NUMBERED BASED ON THE BOVINE PANCREATIC PHOSPHOLIPASE A2. SO, NOT SEQUENTIAL NUMBERS INDICATE DELETIONS AND INSERTIONS REGIONS IN COMPARISON WITH BOVINE PANCREATIC PLA2. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ph4.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ph4.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ph4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2ph4 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2ph4 | HTTPS FTP |
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-Related structure data
Related structure data | 1y4lS 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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Details | The biological assembly is the dimer found in the asymmetric unit. |
-Components
#1: Protein | Mass: 14010.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zhaoermia mangshanensis (snake) / Secretion: venom / References: UniProt: P84776 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.57 Å3/Da / Density % sol: 52.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: polyethylene glycol 8,000; ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→23.87 Å / Num. obs: 17731 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y4L Resolution: 2.05→23.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.84 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.077 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→23.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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