+Open data
-Basic information
Entry | Database: PDB / ID: 4nfc | ||||||
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Title | Structure of paired immunoglobulin-like type 2 receptor (PILR ) | ||||||
Components | Paired immunoglobulin-like type 2 receptor beta | ||||||
Keywords | IMMUNE SYSTEM / IgV-like / immune-related activation receptor / CD99 / cell surface | ||||||
Function / homology | Function and homology information activation of transmembrane receptor protein tyrosine kinase activity / MHC class I protein binding / cell surface receptor protein tyrosine kinase signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lu, Q. / Lu, G. / Qi, J. / Li, Y. / Zhang, Y. / Wang, H. / Fan, Z. / Yan, J. / Gao, G.F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: PILR alpha and PILR beta have a siglec fold and provide the basis of binding to sialic acid Authors: Lu, Q. / Lu, G. / Qi, J. / Wang, H. / Xuan, Y. / Wang, Q. / Li, Y. / Zhang, Y. / Zheng, C. / Fan, Z. / Yan, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nfc.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfc.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfc ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfc | HTTPS FTP |
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-Related structure data
Related structure data | 4nfbSC 4nfdC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14047.961 Da / Num. of mol.: 2 / Fragment: UNP residues 32-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDFACT, PILR, PILRB, PP1551 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKJ0 #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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 291 K / pH: 8.5 Details: 3%(w/v) dextran sulfate sodium salt, 0.1M BICINE pH 8.5, 15%(w/v) polyethylene glycol 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13332 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 17.03 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.789 / Rsym value: 0.465 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NFB Resolution: 2.2→35.65 Å / SU ML: 0.28 / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.65 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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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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