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Yorodumi- PDB-3hef: Crystal structure of the bacteriophage Sf6 terminase small subunit -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hef | ||||||
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Title | Crystal structure of the bacteriophage Sf6 terminase small subunit | ||||||
Components | Gene 1 protein | ||||||
Keywords | VIRAL PROTEIN / bacteriophage Sf6 / terminase small subunit gp1 / gp1 octameric assembly / gp1 channel / DNA recognition / DNA packaging | ||||||
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 | Enterobacteria phage Sf6 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Zhao, H. / Tang, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine Authors: Zhao, H. / Finch, C.J. / Sequeira, R.D. / Johnson, B.A. / Johnson, J.E. / Casjens, S.R. / Tang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hef.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hef.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3hef ftp://data.pdbj.org/pub/pdb/validation_reports/he/3hef | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15859.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage Sf6 (virus) / Gene: gp1 / Plasmid: pET28b / 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: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2M NaH2PO4/0.8M K2HPO4, 0.2M Li2SO4, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 7.2 % / Av σ(I) over netI: 107.12 / Number: 176519 / Rmerge(I) obs: 0.065 / Χ2: 1.8 / D res high: 1.86 Å / D res low: 50 Å / Num. obs: 24582 / % possible obs: 98.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.65→50 Å / Num. all: 35754 / Num. obs: 35647 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 28.4 % / Rmerge(I) obs: 0.053 / Χ2: 1.925 / Net I/σ(I): 107.121 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 28.6 % / Rmerge(I) obs: 0.521 / Num. unique all: 3521 / Χ2: 1.223 / % possible all: 100 |
-Phasing
Phasing dm | FOM : 0.57 / FOM acentric: 0.56 / FOM centric: 0.61 / Reflection: 24251 / Reflection acentric: 21281 / Reflection centric: 2970 | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / σ(F): 1037 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 63.494 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.21 Å2 / Biso mean: 35.237 Å2 / Biso min: 11.69 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019
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Xplor file |
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