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Yorodumi- PDB-1p65: Crystal structure of the nucleocapsid protein of porcine reproduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p65 | ||||||
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Title | Crystal structure of the nucleocapsid protein of porcine reproductive and respiratory syndrome virus (PRRSV) | ||||||
Components | nucleocapsid protein | ||||||
Keywords | VIRAL PROTEIN / virus / nucleocapsid | ||||||
Function / homology | Helix Hairpins - #90 / Arterivirus nucleocapsid / Arterivirus nucleocapsid protein / Nucleocapsid protein, C-terminal / Helix Hairpins / Helix non-globular / Special / viral nucleocapsid / Nucleocapsid protein Function and homology information | ||||||
Biological species | Porcine respiratory and reproductive syndrome virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / S-SAD / Resolution: 2.6 Å | ||||||
Authors | Doan, D.N.P. / Dokland, T. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the nucleocapsid protein of porcine reproductive and respiratory syndrome virus. Authors: Doan, D.N.P. / Dokland, T. #1: Journal: To be Published Title: Cloning, expression, crystallization and preliminary X-ray diffraction analysis of the structural domain of the nucleocapsid N protein from porcine reproductive and respiratory syndrome virus Authors: Doan, D.N.P. / Dokland, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p65.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p65.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p65_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
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Full document | 1p65_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 1p65_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1p65_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p65 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p65 | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 8172.031 Da / Num. of mol.: 2 / Fragment: capsid-forming domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine respiratory and reproductive syndrome virus Genus: Arterivirus / Gene: orf7 / Plasmid: PET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YJI1 #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: 2.21 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal grow | *PLUS Temperature: 15 ℃ |
Components of the solutions | *PLUS Conc.: 8 % / Common name: PEG3350 / Details: pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.74 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 2002 |
Radiation | Monochromator: silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. all: 4813 / Num. obs: 4813 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.6→2.68 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 12 / Num. unique all: 389 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 389 / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: S-SAD / Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.008 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 0.609 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.847 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.708 Å / Total num. of bins used: 12 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.71 Å |