+Open data
-Basic information
Entry | Database: PDB / ID: 1wq9 | |||||||||
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Title | Crystal structure of VR-1, a VEGF-F from a snake venom | |||||||||
Components | (Vascular endothelial growth factor) x 2 | |||||||||
Keywords | TOXIN / Snake venom / Vascular endothelial growth factor / VEGF / VEGF-F | |||||||||
Function / homology | Function and homology information growth factor activity / toxin activity / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Daboia russellii russellii (snake) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | |||||||||
Authors | Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structures of novel vascular endothelial growth factors (VEGF) from snake venoms: insight into selective VEGF binding to kinase insert domain-containing receptor but not to fms-like tyrosine kinase-1. Authors: Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Snake venom vascular endothelial growth factors (VEGFs) exhibit potent activity through their specific recognition of KDR (VEGF receptor 2) Authors: Yamazaki, Y. / Takani, K. / Atoda, H. / Morita, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wq9.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wq9.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/1wq9 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/1wq9 | 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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Details | The biological assembly is dimeric form in a asymmetric unit. |
-Components
#1: Protein | Mass: 10965.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Secretion: venom / Species: Daboia russellii / Strain: russellii / References: UniProt: P67861 |
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#2: Protein | Mass: 10947.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Secretion: venom / Species: Daboia russellii / Strain: russellii / References: UniProt: P67861 |
#3: 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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 6000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 17004 / Num. obs: 15744 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.061 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.236 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 213927.09 / 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: 37.9868 Å2 / ksol: 0.325652 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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