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Yorodumi- PDB-1op0: Crystal Structure of AaV-SP-I, a Glycosylated Snake Venom Serine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1op0 | |||||||||
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Title | Crystal Structure of AaV-SP-I, a Glycosylated Snake Venom Serine Proteinase from Agkistrodon acutus | |||||||||
Components | Venom serine proteinase | |||||||||
Keywords | HYDROLASE / snake venom / serine proteinase / glycoprotein / Agkistrodon acutus | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / toxin activity / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | |||||||||
Biological species | Deinagkistrodon acutus (Chinese moccasin) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Zhu, Z. / Teng, M. / Niu, L. | |||||||||
Citation | ||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1op0.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1op0.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1op0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1op0_validation.pdf.gz | 759.4 KB | Display | wwPDB validaton report |
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Full document | 1op0_full_validation.pdf.gz | 760.2 KB | Display | |
Data in XML | 1op0_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1op0_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1op0 ftp://data.pdbj.org/pub/pdb/validation_reports/op/1op0 | HTTPS FTP |
-Related structure data
Related structure data | 1op2C 1bqyS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 25357.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / Secretion: venom gland References: UniProt: Q9I8X1, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: 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: 2.76 Å3/Da / Density % sol: 55.08 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: lithium sulfate, sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Zhu, Z., (2003) Acta Crystallogr., Sect.D, 59, 547. | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 6, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20865 / Num. obs: 20865 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.123 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 85.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 85.4 % / Rmerge(I) obs: 0.478 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BQY Resolution: 2→36.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 268424.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4156 Å2 / ksol: 0.352518 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 36.1 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.1 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.28 |