+Open data
-Basic information
Entry | Database: PDB / ID: 2bbd | ||||||
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Title | Crystal Structure of the STIV MCP | ||||||
Components | coat protein | ||||||
Keywords | VIRAL PROTEIN / Archaea / hyperthermophile / virus / evolution / crystal | ||||||
Function / homology | viral capsid / Coat protein Function and homology information | ||||||
Biological species | Sulfolobus turreted icosahedral virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Khayat, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Authors: Khayat, R. / Tang, L. / Larson, E.T. / Lawrence, C.M. / Young, M. / Johnson, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bbd.cif.gz | 270 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bbd.ent.gz | 226.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/2bbd ftp://data.pdbj.org/pub/pdb/validation_reports/bb/2bbd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Details | The biological assembly is believed to be a trimer. However, only monomers are observed in the ASU. |
-Components
#1: Protein | Mass: 38744.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus turreted icosahedral virus / Genus: Rudivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q0J0 #2: Chemical | ChemComp-MPD / ( #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: 3.352 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 298.5 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 16% PEG 3350 10% MPD 0.2M Ammonium Citrate (pH 4.5) 5% (v/v) glycerol 2mM DTT 20mM N,N-Dimethyldecylamine-B-oxide 0.1M Bicine (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 298.5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2004 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→30 Å / Num. all: 116333 / Num. obs: 114006 / % possible obs: 83.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.2 Å2 |
Reflection shell | Resolution: 2.04→2.17 Å / % possible all: 50 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→29.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 125966.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.0565 Å2 / ksol: 0.326427 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.17 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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