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Yorodumi- PDB-2vvd: Crystal structure of the receptor binding domain of the spike pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vvd | ||||||
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Title | Crystal structure of the receptor binding domain of the spike protein P1 from bacteriophage PM2 | ||||||
Components | SPIKE PROTEIN P1 | ||||||
Keywords | VIRAL PROTEIN / VIRAL RECEPTOR BINDING DOMAIN | ||||||
Function / homology | Jelly Rolls - #720 / Phage PM2 spike protein P1 / Spike protein P1, first jelly-roll domain / Spike protein P1, second jelly-roll domain / virion component / Jelly Rolls / Sandwich / Mainly Beta / Spike protein P1 Function and homology information | ||||||
Biological species | PSEUDOALTEROMONAS PHAGE PM2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å | ||||||
Authors | Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2. Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vvd.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvd.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vvd_validation.pdf.gz | 411.7 KB | Display | wwPDB validaton report |
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Full document | 2vvd_full_validation.pdf.gz | 411.8 KB | Display | |
Data in XML | 2vvd_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2vvd_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvd ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvd | HTTPS FTP |
-Related 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: 20165.787 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 159-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOALTEROMONAS PHAGE PM2 (virus) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9XJR3 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | FRAGMENT CLONED STARTS AT RESIDUE 159 AND STOPS AT 335 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.94 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 7.4MG/ML PROTEIN (IN 150MM NACL AND 20MM TRIS PH 7.5), 20%(W/V) PEG3350, 200MM CACL2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97912,0.90499 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2005 / Details: MIRRORS | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.26→21.6 Å / Num. obs: 6935 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 14.65 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 46.5 | |||||||||
Reflection shell | Resolution: 2.26→2.33 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 27.7 / % possible all: 52.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.26→21.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.422 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→21.6 Å
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Refine LS restraints |
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