[English] 日本語
Yorodumi- PDB-1m4k: Crystal structure of the human natural killer cell activator rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m4k | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human natural killer cell activator receptor KIR2DS2 (CD158j) | ||||||
Components | KILLER CELL IMMUNOGLOBULIN-LIKE RECEPTOR 2DS2 | ||||||
Keywords | IMMUNE SYSTEM / beta-sandwich / Ig-like C2 type domain | ||||||
Function / homology | Function and homology information stimulatory killer cell immunoglobulin-like receptor signaling pathway / DAP12 interactions / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / immune response / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Saulquin, X. / Gastinel, L.N. / Vivier, E. | ||||||
Citation | Journal: J.EXP.MED. / Year: 2003 Title: Crystal structure of the human natural killer cell activating receptor KIR2DS2 (CD158j) Authors: Saulquin, X. / Gastinel, L.N. / Vivier, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m4k.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m4k.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1m4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4k ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4k | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22048.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P43631 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Ammonium sulfate, sodium acetate, Zinc chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 17624 / Num. obs: 17624 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.78 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.1→2.3 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.286 / % possible all: 99.6 |
Reflection | *PLUS % possible obs: 61 % / Rmerge(I) obs: 0.48 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: KIR2dL2, KIR2DL1, KIR2DL3 Resolution: 2.3→28.16 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.16 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021
| |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28 Å | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
|