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Yorodumi- PDB-4esk: Crystal structure of a strand-swapped dimer of Mouse Leukocyte-as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4esk | ||||||
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Title | Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 (NYSGRC-006047)IG-like domain | ||||||
Components | Leukocyte-associated immunoglobulin-like receptor 1 | ||||||
Keywords | IMMUNE SYSTEM / LAIR-1 / IG-like domain / Domain swapping / Collagen Receptor / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / Collagen / cell surface / Atoms-to-Animals: The Immune Function Network / IFN | ||||||
Function / homology | Function and homology information Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å | ||||||
Authors | Sampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN) | ||||||
Citation | Journal: to be published Title: Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 IG-like domain Authors: Sampathkumar, P. / Bonanno, J. / Fiser, A. / Patskovsky, Y. / Zencheck, W. / Nathenson, S.G. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4esk.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4esk.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 4esk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4esk ftp://data.pdbj.org/pub/pdb/validation_reports/es/4esk | HTTPS FTP |
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-Related structure data
Related structure data | 4etyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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7 |
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Unit cell |
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-Components
#1: Protein | Mass: 11611.049 Da / Num. of mol.: 4 / Fragment: UNP Residues 22-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lair1 / Plasmid: pNIC28-Bas4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: Q8BG84 #2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | #5: 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: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 6 Details: Protein (8.5mg/ml in 20 mM Trizma Base pH 8.2, 100 mM NaCl; Reservoir (1.0 M K/Na tartrate MES pH 6.0 - Wizard I & II #98); Cryoprotection (30% glycerol in Reservior solution), Sitting Drop ...Details: Protein (8.5mg/ml in 20 mM Trizma Base pH 8.2, 100 mM NaCl; Reservoir (1.0 M K/Na tartrate MES pH 6.0 - Wizard I & II #98); Cryoprotection (30% glycerol in Reservior solution), Sitting Drop Vapor Diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011 / Details: MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→38.51 Å / Num. all: 41765 / Num. obs: 40723 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.043 / Net I/σ(I): 59.3 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 1762 / Rsym value: 0.363 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ETY Resolution: 1.762→38.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.225 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 55.12 Å2 / Biso mean: 20.6285 Å2 / Biso min: 8.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.762→38.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.762→1.808 Å / Total num. of bins used: 20
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