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Yorodumi- PDB-5oe9: Structure of large terminase from the thermophilic bacteriophage ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oe9 | |||||||||
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Title | Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (Crystal form 2) | |||||||||
Components | Large subunit terminase | |||||||||
Keywords | VIRAL PROTEIN / large terminase | |||||||||
Function / homology | Bacteriophage terminase, large subunit / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Large subunit terminase Function and homology information | |||||||||
Biological species | Deep-sea thermophilic phage D6E (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 | 5oe9.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oe9.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 5oe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oe9 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oe9 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 50166.492 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deep-sea thermophilic phage D6E (virus) Production host: Escherichia coli (E. coli) / References: UniProt: E5DV50 #2: Chemical | ChemComp-SO4 / #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: 2.88 Å3/Da / Density % sol: 57.24 % |
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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: I04-1 / Wavelength: 0.9282 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.38→46.65 Å / Num. obs: 64217 / % possible obs: 97.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Net I/σ(I): 13.5 / Num. measured all: 268569 / Scaling rejects: 5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.4→46.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.911 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.233 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: 162.52 Å2 / Biso mean: 69.991 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.4→46.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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