+Open data
-Basic information
Entry | Database: PDB / ID: 1j2l | ||||||
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Title | Crystal structure of the disintegrin, trimestatin | ||||||
Components | Disintegrin triflavin | ||||||
Keywords | TOXIN / disintegrin / RGD motif / trimestatin / snake venom | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trimeresurus flavoviridis (habu) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fujii, Y. / Okuda, D. / Fujimoto, Z. / Morita, T. / Mizuno, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of Trimestatin, a Disintegrin Containing a Cell Adhesion Recognition Motif RGD Authors: Fujii, Y. / Okuda, D. / Fujimoto, Z. / Horii, T. / Morita, T. / Mizuno, H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and preliminary crystallographic studies of dimeric disintegrins from the venom of two Agkistrodon snakes. Authors: Fujii, Y. / Okuda, D. / Fujimoto, Z. / Morita, T. / Mizuno, H. #2: Journal: J.Biochem.(Tokyo) / Year: 2001 Title: Purification and characterization of a new RGD/KGD-containing dimeric disintegrin, piscivostatin, from the venom of Agkistrodon piscivorus piscivorus: the unique effect of piscivostatin on platelet aggregation. Authors: Okuda, D. / Morita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j2l.cif.gz | 28.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2l.ent.gz | 18.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2l ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2l | HTTPS FTP |
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-Related structure data
Related structure data | 1fvlS 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: 7586.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P21859 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.2 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: PEG 8000, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 7539 / Num. obs: 52379 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.056 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1092 / Rsym value: 0.242 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. obs: 7539 / Num. measured all: 52379 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Lowest resolution: 1.76 Å / Num. unique obs: 1092 / Num. measured obs: 7548 / Rmerge(I) obs: 0.242 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FVL Resolution: 1.7→18.31 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1415224.78 / 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: 40.1676 Å2 / ksol: 0.33892 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→18.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection all: 52379 / Num. reflection obs: 7538 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.278 / Rfactor Rwork: 0.229 / Num. reflection Rwork: 737 |