+Open data
-Basic information
Entry | Database: PDB / ID: 8qgr | ||||||
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Title | Stopper protein of phage 812 in closed conformation | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS / phage / neck / connector | ||||||
Function / homology | Capsid protein Function and homology information | ||||||
Biological species | Staphylococcus phage 812 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cienikova, Z. / Popelarova, B. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: To Be Published Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812 Authors: Cienikova, Z. / Novacek, J. / Siborova, M. / Popelarova, B. / Fuzik, T. / Benesik, M. / Bardy, P. / Plevka, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qgr.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qgr.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qgr_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 8qgr_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | 8qgr_validation.xml.gz | 13 KB | Display | |
Data in CIF | 8qgr_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/8qgr ftp://data.pdbj.org/pub/pdb/validation_reports/qg/8qgr | HTTPS FTP |
-Related structure data
Related structure data | 8q01C 8q1iC 8q7dC 8qekC 8qemC 8qjeC 8qkhC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 33757.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus phage 812 (virus) / Strain: K1-420 Gene: 812_097, 812_099, 812a_099, 812F1_099, K1/420_099, K1_099 Plasmid: pET22T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1YTN7 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M NaCl, 8% PEG 6000, 20% glycerol, 3% dextran sulphate sodium |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2017 |
Radiation | Monochromator: Si(111) single-crystal channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.2 Å / Num. obs: 16664 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 23.26 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 1627 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.159 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.172 / SU B: 5.096 / SU ML: 0.127 / Average fsc free: 0.9603 / Average fsc work: 0.9703 / Cross valid method: FREE R-VALUE / ESU R: 0.226 / ESU R Free: 0.18 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.435 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→37.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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