+Open data
-Basic information
Entry | Database: PDB / ID: 7x4v | ||||||
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Title | Crystal structure of Rhodostomin ARGDDP mutant | ||||||
Components | Disintegrin rhodostomin | ||||||
Keywords | BLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Calloselasma rhodostoma (Malayan pit viper) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Chang, Y.T. / Chuang, W.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To be published Title: Crystal structure of Rhodostomin ARGDDP mutant Authors: Chang, Y.T. / Chuang, W.J. #1: Journal: PLoS One / Year: 2017 Title: Effects of the RGD loop and C-terminus of rhodostomin on regulating integrin alphaIIbbeta3 recognition Authors: Chang, Y.T. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x4v.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x4v.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 7x4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x4v_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 7x4v_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 7x4v_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7x4v_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/7x4v ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x4v | HTTPS FTP |
-Related structure data
Related structure data | 4rqgS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7299.216 Da / Num. of mol.: 2 / Mutation: P455A, M459D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper) Production host: Pichia (fungus) / References: UniProt: P30403 #2: 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: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M NH4OAc, 0.05 M Sodium cacodylate pH 6.5, 30% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30 Å / Num. obs: 32038 / % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.38→1.43 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 3211 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RQG Resolution: 1.38→18.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.246 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.221 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→18.09 Å
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Refine LS restraints |
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