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Yorodumi- PDB-5jfb: Crystal structure of the scavenger receptor cysteine-rich domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfb | ||||||
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Title | Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163 | ||||||
Components | Scavenger receptor cysteine-rich type 1 protein M130 | ||||||
Keywords | ENDOCYTOSIS / CD163 / SRCR / PRRSV | ||||||
Function / homology | Function and homology information acute-phase response / virus receptor activity / external side of plasma membrane / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ma, H. / Jiang, L. / Qiao, S. / Zhang, G. / Li, R. | ||||||
Citation | Journal: J. Virol. / Year: 2017 Title: The Crystal Structure of the Fifth Scavenger Receptor Cysteine-Rich Domain of Porcine CD163 Reveals an Important Residue Involved in Porcine Reproductive and Respiratory Syndrome Virus Infection Authors: Ma, H. / Jiang, L. / Qiao, S. / Zhi, Y. / Chen, X.X. / Yang, Y. / Huang, X. / Huang, M. / Li, R. / Zhang, G.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jfb.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jfb.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfb ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfb | HTTPS FTP |
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-Related structure data
Related structure data | 1by2S S: Starting model for refinement |
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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: 12083.336 Da / Num. of mol.: 1 / Fragment: SRCR 5 domain, UNP residues 477-577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CD163, M130 / Plasmid: pMT/BiP/Blast / Cell line (production host): SCHNEIDER'S S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q2VL90 |
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#2: 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: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25% (w/v) PEG 4000, 200mM (NH4)2SO4 in 100mM sodium acetate at pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: Pilatus / Detector: CMOS / Date: Sep 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 6682 / % possible obs: 97.1 % / Redundancy: 10 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2→2.07 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BY2 Resolution: 2→43.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.562 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.177 / 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: 23.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.76 Å
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Refine LS restraints |
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