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Yorodumi- PDB-4kfr: Structure of the genome packaging NTPase B204 from Sulfolobus tur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kfr | ||||||
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Title | Structure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with sulfate | ||||||
Components | Genome packaging NTPase B204 | ||||||
Keywords | HYDROLASE / FtsK-HerA superfamily / P-loop ATPase / genome packaging NTPase | ||||||
Function / homology | P-loop containing nucleotide triphosphate hydrolases / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Sulfolobus turreted icosahedral virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.956 Å | ||||||
Authors | Happonen, L.J. / Oksanen, E. / Goldman, A. / Kajander, T. / Butcher, S. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2. Authors: Happonen, L.J. / Oksanen, E. / Liljeroos, L. / Goldman, A. / Kajander, T. / Butcher, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kfr.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kfr.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 4kfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/4kfr ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kfr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24907.756 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus turreted icosahedral virus 2 Gene: B204, STIV2_B204 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566/pTF16 / References: UniProt: D5IEZ9, Hydrolases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / | #4: 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: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M sodium cacodylate, 0.21 M ammonium sulfate, 0.05 M magnesium chloride, protein in 50 mM sodium citrate, 35% PEG6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.979790,0.979860,0.979110 | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2011 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.956→48.587 Å / Num. all: 58758 / Num. obs: 58758 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Biso Wilson estimate: 28.35 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14 | ||||||||||||
Reflection shell | Resolution: 1.956→2.07 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.15 / Num. unique all: 9283 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.956→48.587 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 21.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.956→48.587 Å
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Refine LS restraints |
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LS refinement shell |
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