+Open data
-Basic information
Entry | Database: PDB / ID: 6jds | ||||||
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Title | Crystal structure of truncated PRRSV nsp10 (helicase) | ||||||
Components | PP1b | ||||||
Keywords | VIRAL PROTEIN / Helicase / ATPase / Truncated | ||||||
Function / homology | Function and homology information host cell membrane / RNA nuclease activity / endonuclease activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding ...host cell membrane / RNA nuclease activity / endonuclease activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Porcine reproductive and respiratory syndrome virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Tang, C. / Chen, Z. | ||||||
Citation | Journal: Viruses / Year: 2020 Title: Helicase of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Strain HV Reveals a Unique Structure. Authors: Tang, C. / Deng, Z. / Li, X. / Yang, M. / Tian, Z. / Chen, Z. / Wang, G. / Wu, W. / Feng, W.H. / Zhang, G. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jds.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jds.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jds_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 6jds_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 6jds_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6jds_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jds ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jds | HTTPS FTP |
-Related structure data
Related structure data | 6jdrSC 6jduC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29878.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus Production host: Escherichia coli (E. coli) / References: UniProt: J9XNG9 | ||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 5000 MME, 1-propanol, MES |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 15236 / % possible obs: 99.6 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.022 / Rrim(I) all: 0.083 / Net I/σ(I): 36.44 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 14 % / Num. unique obs: 703 / Rpim(I) all: 0.226 / Rrim(I) all: 0.858 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDR Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.562 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.227 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.967 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→50 Å
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Refine LS restraints |
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