[English] 日本語
Yorodumi- PDB-5xor: Crystal structure of N-terminal replicase protein of porcine circ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xor | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of N-terminal replicase protein of porcine circovirus type 2 | ||||||
Components | Rep protein | ||||||
Keywords | REPLICATION / PCV2 / Rep / Dimer | ||||||
Function / homology | Function and homology information : / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / nucleotidyltransferase activity / DNA replication / RNA helicase activity / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Porcine circovirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å | ||||||
Authors | Song, Y. / Peng, G. | ||||||
Citation | Journal: J. Virol. / Year: 2018 Title: Crystal Structure of the Dimerized N Terminus of Porcine Circovirus Type 2 Replicase Protein Reveals a Novel Antiviral Interface Authors: Luo, G. / Zhu, X. / Lv, Y. / Lv, B. / Fang, J. / Cao, S. / Chen, H. / Peng, G. / Song, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xor.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xor.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xor_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xor_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 5xor_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 5xor_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xor ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xor | HTTPS FTP |
-Related structure data
Related structure data | 2hw0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18077.359 Da / Num. of mol.: 5 / Fragment: UNP residues 1-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine circovirus 2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A9YPG7 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.1M HEPES sodium pH 8.0, 0.45 M sodium citrate tribasic dihydrate, 50% (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 46536 / % possible obs: 97.9 % / Redundancy: 4.4 % / Net I/σ(I): 12.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2hw0 Resolution: 2.699→42.34 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.62 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.699→42.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|