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Yorodumi- PDB-4ife: Crystal Structure of the large terminase subunit gp2 of bacterial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ife | ||||||
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Title | Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6 complexed with ATP | ||||||
Components | Gene 2 protein | ||||||
Keywords | VIRAL PROTEIN / DNA packaging / terminase / ATPase / nuclease / ATP binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella phage Sf6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.05 Å | ||||||
Authors | Zhao, H. / Christensen, T. / Kamau, Y. / Tang, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Authors: Zhao, H. / Christensen, T.E. / Kamau, Y.N. / Tang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ife.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ife.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ife.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ife ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ife | HTTPS FTP |
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-Related structure data
Related structure data | 4idhSC 4ieeC 4ieiC 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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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
-Components
#1: Protein | Mass: 55333.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella phage Sf6 (virus) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q716H3 |
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#2: Chemical | ChemComp-ATP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris, 15% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→100 Å / Num. obs: 9962 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 66.02 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 21.02 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5.08 / Num. unique all: 366 / % possible all: 64.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4IDH Resolution: 3.05→19.904 Å / SU ML: 0.4 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.75 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→19.904 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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