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Yorodumi- PDB-1umr: Crystal structure of the platelet activator convulxin, a disulfid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1umr | ||||||
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Title | Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / LECTIN / C-TYPE LECTIN / PLATELET / SUGAR-BINDING PROTEIN / ACTIVATOR / SNAKE VENOM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Murakami, M.T. / Zela, S.P. / Gava, L.M. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2003 Title: Crystal Structure of the Platelet Activator Convulxin, a Disulfide Linked A4B4 Cyclic Tetramer from the Venom of Crotalus Durissus Terrificus Authors: Murakami, M.T. / Zela, S.P. / Gava, L.M. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Initial Structural Analysis of an Alpha(4)Beta(4) C-Type Lectin from the Venom of Crotalus Durissus Terrificus Authors: Murakami, M.T. / Watanabe, L. / Gava, L.M. / Zela, S.P. / Cintra, A.C.O. / Arni, R.K. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1umr.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1umr.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 1umr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1umr_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 1umr_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 1umr_validation.xml.gz | 26 KB | Display | |
Data in CIF | 1umr_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1umr ftp://data.pdbj.org/pub/pdb/validation_reports/um/1umr | HTTPS FTP |
-Related structure data
Related structure data | 1c3aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | THE QUATERNARY STRUCTURE IS OF THE TYPE A4B4 CYCLICTETRAMER (HETERO-OCTAMERIC) |
-Components
#1: Protein | Mass: 15745.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake) Tissue: VENOM GLAND / References: UniProt: O93426 #2: Protein | Mass: 14960.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake) Tissue: VENOM GLAND / References: UniProt: O93427 #3: 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: 4.8 Å3/Da / Density % sol: 73 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 36900 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.4→2.6 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3A Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.669 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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