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Open data
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Basic information
Entry | Database: PDB / ID: 8h7j | ||||||
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Title | The crystal structure of CD163 SRCR5-9 | ||||||
![]() | Scavenger receptor cysteine-rich type 1 protein M130 | ||||||
![]() | ENDOCYTOSIS / CD163 / arterivirus receptor / SRCR / long-range SRCR repeat / putative arterivirus interaction domains | ||||||
Function / homology | ![]() zymogen activation / acute-phase response / virus receptor activity / external side of plasma membrane / serine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, Z.P. / Li, R. / Ma, H.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of CD163 SRCR5-9 Authors: Ma, H.F. / Li, R. / Luo, Z.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.6 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jfbS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60516.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 4000, 0.15M potassium sodium tartrate tetra-hydrate pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 20350 / % possible obs: 98.7 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.059 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1962 / CC1/2: 0.761 / Rpim(I) all: 0.779 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JFB Resolution: 2.5→48.487 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.676 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 1.026 / ESU R Free: 0.268 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.455 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.487 Å
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Refine LS restraints |
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LS refinement shell |
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