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Yorodumi- PDB-4znk: Thermus Phage P74-26 Large Terminase ATPase domain from (P 32 2 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4znk | |||||||||
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Title | Thermus Phage P74-26 Large Terminase ATPase domain from (P 32 2 1 space group) | |||||||||
Components | Phage terminase large subunit | |||||||||
Keywords | VIRAL PROTEIN / DNA Translocation | |||||||||
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 P7426 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 Å | |||||||||
Authors | Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Kelch, B.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structure and mechanism of the ATPase that powers viral genome packaging. Authors: Hilbert, B.J. / Hayes, J.A. / Stone, N.P. / Duffy, C.M. / Sankaran, B. / Kelch, B.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4znk.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4znk.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 4znk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/4znk ftp://data.pdbj.org/pub/pdb/validation_reports/zn/4znk | HTTPS FTP |
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-Related structure data
Related structure data | 4zniSC 4znjC 4znlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31580.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p84 / Plasmid: pet24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR DE3 / References: UniProt: A7XXR1 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 11% (w/v) PEG 2000, 0.15 M ammonium sulfate, and 0.1 M tri-sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.931→34.4 Å / Num. obs: 23556 / % possible obs: 99.68 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 1.931→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.96 / % possible all: 97.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZNI Resolution: 1.931→34.398 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.931→34.398 Å
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Refine LS restraints |
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LS refinement shell |
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