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Yorodumi- PDB-4iei: Crystal Structure of the large terminase subunit gp2 of bacterial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iei | ||||||
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Title | Crystal Structure of the large terminase subunit gp2 of bacterial virus Sf6 complexed with ADP | ||||||
Components | Gene 2 protein | ||||||
Keywords | VIRAL PROTEIN / DNA packaging / terminase / ATPase / nuclease / ADP binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella phage Sf6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.09 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 | 4iei.cif.gz | 197.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iei.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 4iei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/4iei ftp://data.pdbj.org/pub/pdb/validation_reports/ie/4iei | HTTPS FTP |
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-Related structure data
Related structure data | 4idhSC 4ieeC 4ifeC 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: 55247.500 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-ADP / |
#3: 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: 2.46 Å3/Da / Density % sol: 50.04 % |
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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-D / Wavelength: 1.00318 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2012 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00318 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→29.12 Å / Num. obs: 32795 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2232 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4IDH Resolution: 2.09→19.783 Å / SU ML: 0.25 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.5 / 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: 39.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→19.783 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.4158 Å / Origin y: 40.2896 Å / Origin z: 49.0004 Å
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Refinement TLS group | Selection details: ALL |