+Open data
-Basic information
Entry | Database: PDB / ID: 7cn6 | |||||||||
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Title | T4 phage spackle protein gp61.3 | |||||||||
Components | Protein spackle | |||||||||
Keywords | VIRAL PROTEIN / Lysozyme inhibitor / Phage Lysis inhibition | |||||||||
Function / homology | Protein spackle / superinfection exclusion / host cell periplasmic space / Protein spackle Function and homology information | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | |||||||||
Authors | Kanamaru, S. / Leiman, P.G. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Viruses / Year: 2020 Title: Structure and Function of the T4 Spackle Protein Gp61.3. Authors: Kanamaru, S. / Uchida, K. / Nemoto, M. / Fraser, A. / Arisaka, F. / Leiman, P.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cn6.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cn6.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/7cn6 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/7cn6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8876.365 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: sp, 61.3 / Plasmid: pUC19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39230 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.01 Å3/Da / Density % sol: 38.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.4 / Details: PEG4000, glycine, calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2009 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.8 Å / Num. obs: 51366 / % possible obs: 95.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.76 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.107 / Rrim(I) all: 0.151 / Χ2: 0.83 / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1001 / CC1/2: 0.895 / Rpim(I) all: 0.19 / Rrim(I) all: 0.269 / Χ2: 0.47 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→19.9 Å / SU ML: 0.1797 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 28.4219 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.9 Å
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Refine LS restraints |
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LS refinement shell |
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