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Yorodumi- PDB-8xms: Crystal structure of Porcine Circovirus type II Rep ATPase domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xms | ||||||
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Title | Crystal structure of Porcine Circovirus type II Rep ATPase domain | ||||||
Components | Replication-associated protein | ||||||
Keywords | VIRAL PROTEIN / Replication / ATPase / Viral protein. | ||||||
Function / homology | Function and homology information rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity ...rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Porcine circovirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Guan, S.Y. / Song, Y.F. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Gen.Virol. / Year: 2024 Title: Crystal structure of the ATPase domain of porcine circovirus type 2 Rep protein. Authors: Guan, S. / Li, Z. / Han, Y. / Tian, A. / Zhou, S. / Chen, H. / Peng, G. / Song, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xms.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xms.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 8xms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xms_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
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Full document | 8xms_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 8xms_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 8xms_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/8xms ftp://data.pdbj.org/pub/pdb/validation_reports/xm/8xms | 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 18852.090 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine circovirus 2 / Gene: Rep, ORF1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8BB16, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'- ...References: UniProt: Q8BB16, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #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: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS PH6.0, 0.2M Li2SO4, 22% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.95915 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Jan 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95915 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→59.33 Å / Num. obs: 50956 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 4415 / CC1/2: 0.944 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.33 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.866 / SU B: 9.429 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.462 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→59.33 Å
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