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Yorodumi- PDB-1y17: crystal structure of Aa-X-bp-II, a snake venom protein with the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y17 | ||||||
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Title | crystal structure of Aa-X-bp-II, a snake venom protein with the activity of binding to coagulation factor X from Agkistrodon acutus | ||||||
Components |
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Keywords | BLOOD CLOTTING / Aa-X-bp-II / C-type lectin-like proteins / snake venom / Agkistrodon acutus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinagkistrodon acutus (Chinese moccasin) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zhu, Z. / Liu, S. / Mo, X. / Yu, X. / Liang, Z. / Zang, J. / Zhao, W. / Teng, M. / Niu, L. | ||||||
Citation | Journal: To be Published Title: Characterizations and Crystal structures of two snake venom proteins with the activity of binding coagulation factor X from Agkistrodon acutus Authors: Zhu, Z. / Liu, S. / Mo, X. / Yu, X. / Liang, Z. / Zang, J. / Zhao, W. / Teng, M. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y17.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y17.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1y17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y17 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y17 | HTTPS FTP |
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-Related 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: 14714.385 Da / Num. of mol.: 1 / Fragment: residues 1-129 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q9DEF9 | ||
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#2: Protein | Mass: 14580.163 Da / Num. of mol.: 1 / Fragment: residues 1-123 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q9DEF8 | ||
#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: 2.16 Å3/Da / Density % sol: 43.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG MME 550, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
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 | Biso Wilson estimate: 19.2 Å2 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.08 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 311524.52 / 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: 23.7233 Å2 / ksol: 0.312668 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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