+Open data
-Basic information
Entry | Database: PDB / ID: 8h56 | ||||||
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Title | Crystal structure of Rep' of porcine circovirus type 2 | ||||||
Components | Isoform Rep' of Replication-associated protein | ||||||
Keywords | VIRAL PROTEIN / Replication / dimer | ||||||
Function / homology | Function and homology information rolling circle single-stranded viral DNA replication / 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 / endonuclease activity / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity ...rolling circle single-stranded viral DNA replication / 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 / endonuclease activity / 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: 2.33 Å | ||||||
Authors | Guan, S.Y. / Song, Y.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Proteins / Year: 2023 Title: Crystal structure of the dimerized of porcine circovirus type II replication-related protein Rep'. Authors: Guan, S. / Tian, A. / Jing, H. / Yuan, H. / Jia, H. / Shi, Y. / Chen, H. / Cao, S. / 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 | 8h56.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h56.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/8h56 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h56 | HTTPS FTP |
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-Related structure data
Related structure data | 5xorS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21343.074 Da / Num. of mol.: 2 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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, pH 7.0, 0.1M Sodium chloride, 1.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→57.24 Å / Num. obs: 18281 / % possible obs: 99.7 % / Redundancy: 14.8 % / CC1/2: 0.999 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.33→2.39 Å / Rmerge(I) obs: 0.444 / Num. unique obs: 1287 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XOR Resolution: 2.33→46 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.51 / 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 max: 126.07 Å2 / Biso mean: 47.4977 Å2 / Biso min: 13.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→46 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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