+Open data
-Basic information
Entry | Database: PDB / ID: 8fr5 | ||||||
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Title | Crystal structure of the Human Smacovirus 1 Rep domain | ||||||
Components | Rep | ||||||
Keywords | REPLICATION / DNA binding protein / endonuclease / viral protein | ||||||
Function / homology | : / Rep Function and homology information | ||||||
Biological species | Human smacovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Limon, L.K. / Shi, K. / Dao, A. / Rugloski, J. / Tompkins, K.J. / Aihara, H. / Gordon, W.R. / Evans IIII, R.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: The crystal structure of the human smacovirus 1 Rep domain. Authors: Limon, L.K. / Shi, K. / Dao, A. / Rugloski, J. / Tompkins, K.J. / Aihara, H. / Gordon, W.R. / Evans 3rd, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fr5.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fr5.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fr5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8fr5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8fr5_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 8fr5_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/8fr5 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/8fr5 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 11533.931 Da / Num. of mol.: 1 / Mutation: Y81F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human smacovirus 1 / Strain: France/2/2008/2548 / Gene: Rep / Plasmid: pTD68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B5CMT4 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MN / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Sodium Acetate pH 5.0, 20% PEG 4000, 1 M Guanidine HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→29.43 Å / Num. obs: 19703 / % possible obs: 95.46 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04161 / Rpim(I) all: 0.02461 / Rrim(I) all: 0.04858 / Net I/σ(I): 14.08 |
Reflection shell | Resolution: 1.33→1.378 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8219 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 5923 / CC1/2: 0.757 / CC star: 0.928 / Rpim(I) all: 0.5037 / Rrim(I) all: 0.9694 / % possible all: 82.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→29.43 Å / SU ML: 0.1788 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8462 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 27.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→29.43 Å
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Refine LS restraints |
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LS refinement shell |
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