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Yorodumi- PDB-5oee: Structure of large terminase from the thermophilic bacteriophage ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oee | |||||||||
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Title | Structure of large terminase from the thermophilic bacteriophage D6E (Crystal form 3) | |||||||||
Components | Large subunit terminase | |||||||||
Keywords | VIRAL PROTEIN / large terminase | |||||||||
Function / homology | Bacteriophage terminase, large subunit / Terminase large subunit, T4likevirus-type, N-terminal / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / Large subunit terminase Function and homology information | |||||||||
Biological species | Phage D6E (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Xu, R.G. / Jenkins, H.T. / Greive, S.J. / Antson, A.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis. Authors: Xu, R.G. / Jenkins, H.T. / Antson, A.A. / Greive, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oee.cif.gz | 489.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oee.ent.gz | 402.2 KB | Display | PDB format |
PDBx/mmJSON format | 5oee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oee_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 5oee_full_validation.pdf.gz | 475 KB | Display | |
Data in XML | 5oee_validation.xml.gz | 80.5 KB | Display | |
Data in CIF | 5oee_validation.cif.gz | 110.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oee ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oee | HTTPS FTP |
-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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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 49022.129 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phage D6E (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: E5DV50 #2: Chemical | ChemComp-NA / #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: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M Ammonium Sulfate, 0.1 M HEPES pH 8.0 / PH range: 6.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.6→45.69 Å / Num. obs: 91259 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.065 / Rrim(I) all: 0.122 / Net I/σ(I): 7.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.687 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.927 / ESU R Free: 0.326 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.82 Å2 / Biso mean: 69.228 Å2 / Biso min: 23.41 Å2
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Refinement step | Cycle: final / Resolution: 2.6→45.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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