+Open data
-Basic information
Entry | Database: PDB / ID: 2vrs | ||||||
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Title | Structure of avian reovirus sigmaC117-326, C2 crystal form | ||||||
Components | SIGMA-C CAPSID PROTEIN | ||||||
Keywords | VIRAL PROTEIN / ALPHA-HELICAL COILED COIL / RECEPTOR-BINDING / TRIPLE BETA-SPIRAL / VIRION / COILED COIL / BETA-BARREL | ||||||
Function / homology | Function and homology information viral capsid / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | AVIAN REOVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Benavente, J. / van Raaij, M.J. | ||||||
Citation | Journal: J. Gen. Virol. / Year: 2009 Title: Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre. Authors: Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / van Raaij, M.J. #1: Journal: Acta Crystallogr., Sect.F / Year: 2005 Title: Crystallization of the C-Terminal Globular Domain of Avian Reovirus Fibre. Authors: van Raaij, M.J. / Hermo-Parrado, X.L. / Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J. #2: Journal: J.Mol.Biol. / Year: 2005 Title: Structure of the Carboxy-Terminal Receptor-Binding Domain of Avian Reovirus Fibre Sigmac. Authors: Guardado-Calvo, P. / Fox, G.C. / Hermo-Parrado, X.L. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC", "CB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC", "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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 | 2vrs.cif.gz | 153.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrs.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrs ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrs | HTTPS FTP |
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-Related structure data
Related structure data | 2jjlC 2bsfS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 22587.023 Da / Num. of mol.: 3 / Fragment: RESIDUES 117-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AVIAN REOVIRUS / Strain: S1133 Description: THE AVIAN REOVIRUS STRAIN S1133 WAS ORIGINALLY PROVIDED BY DR. PHILIP I.MARCUS WHEN DR. J.BENAVENTE WAS A ROCHE VISITING SCIENTIST IN THE LABORATORY OF DR. A.SHATKIN Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q992I2 |
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-Non-polymers , 5 types, 988 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FIRST RESIDUE, ILE-116, IS A REMNANT OF THE EXPRESSION |
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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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 8.4 Details: 0.6-0.75 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.4, 25% GLYCEROL, 50 MM ZINC SULPHATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.8266 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 3, 2007 / Details: RD COATED FLAT AND TOROIDAL MIRRORS |
Radiation | Monochromator: SI111 DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 90954 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BSF Resolution: 1.75→18.43 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.051 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 117-121 OF CHAIN A AND CHAIN B ARE DISORDERED.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→18.43 Å
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Refine LS restraints |
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