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Yorodumi- PDB-4dyr: Crystal structure of terminase small subunit gp1 of the bacterial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyr | ||||||
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Title | Crystal structure of terminase small subunit gp1 of the bacterial virus sf6 with CAPS PH10.5 buffer | ||||||
Components | Gene 1 protein | ||||||
Keywords | VIRAL PROTEIN / gp1 / octamer / DNA-binding / CAPS buffer | ||||||
Function / homology | : / Bacteriophage Sf6, terminase small subunit-like / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / identical protein binding / Gene 1 protein Function and homology information | ||||||
Biological species | Shigella phage Sf6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Zhao, H. / Tang, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity. Authors: Zhao, H. / Kamau, Y.N. / Christensen, T.E. / Tang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dyr.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyr.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyr ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyr | HTTPS FTP |
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-Related structure data
Related structure data | 4dycC 4dyqC 4dzjC 4dzpC 3hefS 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
#1: Protein | Mass: 15576.782 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella phage Sf6 (virus) / Strain: bacteriophage Sf6 / Gene: gp1 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: Q716H4 #2: 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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 1.2M NAH2PO4/0.8M K2HPO4, 0.2M Li2SO4, 0.1M CAPS pH 10.5, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2009 Details: flat collimating Rh coated mirror, toroidal focussing mirror |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 35672 / Num. obs: 34923 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 22.278 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 48.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.06 / Num. unique all: 3296 / Rsym value: 0.381 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HEF Resolution: 1.65→19.168 Å / SU ML: 0.2 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.552 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.168 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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