+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ptv | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NK cell receptor ligand CD48 | ||||||
![]() | CD48 antigen![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() natural killer cell activation involved in immune response / mast cell activation / Cell surface interactions at the vascular wall / MHC class I protein binding / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, L. / Velikovsky, C.A. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Structure of natural killer receptor 2B4 bound to CD48 reveals basis for heterophilic recognition in signaling lymphocyte activation molecule family. Authors: Velikovsky, C.A. / Deng, L. / Chlewicki, L.K. / Fernandez, M.M. / Kumar, V. / Mariuzza, R.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 34.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 23.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2pttSC ![]() 2ptuC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The biological assembly is the monomer in the asymmetric unit. |
-
Components
#1: Protein | ![]() Mass: 12940.734 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type1, D1, 2B4-binding domain / Mutation: T34Y, K52R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.49 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 30% (w/v) PEG 8000, 100 mM sodium imidazole, 0.2 M NaCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.66→50 Å / Num. obs: 11309 / % possible obs: 97.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 66.7 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / Num. unique all: 1041 / % possible all: 81.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2PTT Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.524 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 25.242 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
|