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Yorodumi- PDB-5m1f: Crystal structure of the large terminase nuclease from thermophil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m1f | |||||||||
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Title | Crystal structure of the large terminase nuclease from thermophilic phage G20c | |||||||||
Components | Phage terminase large subunit | |||||||||
Keywords | VIRAL PROTEIN / large terminase / nuclease domain / hydrolase | |||||||||
Function / homology | Function and homology information viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermus phage G20c (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | |||||||||
Authors | Xu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Greive, S.J. / Antson, A.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Authors: Xu, R.G. / Jenkins, H.T. / Chechik, M. / Blagova, E.V. / Lopatina, A. / Klimuk, E. / Minakhin, L. / Severinov, K. / Greive, S.J. / Antson, A.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m1f.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m1f.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/5m1f ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m1f | HTTPS FTP |
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-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: 21174.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage G20c (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXR1, UniProt: A0A1L4BKS3*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Lithium Sulfate, 0.1 M Bis-tris pH 5.5, 25% PEG3350 |
-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: Jan 21, 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: 2.15→47.72 Å / Num. obs: 9183 / % possible obs: 95.6 % / Redundancy: 2.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.035 / Rrim(I) all: 0.055 / Net I/σ(I): 10.3 / Num. measured all: 20099 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→47.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.194 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.4 Å2 / Biso mean: 54.596 Å2 / Biso min: 29.5 Å2
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Refinement step | Cycle: final / Resolution: 2.15→47.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.147→2.203 Å / Total num. of bins used: 20
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