[English] 日本語
Yorodumi- PDB-2box: EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2box | ||||||
---|---|---|---|---|---|---|---|
Title | EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with strontium. | ||||||
Components | EGF-LIKE MODULE CONTAINING MUCIN-LIKE HORMONE RECEPTOR-LIKE 2 PRECURSOR | ||||||
Keywords | IMMUNE SYSTEM / CD97 / CD55 / 7TM / CALCIUM-BINDING / CELL ADHESION / EGF-LIKE DOMAIN / G-PROTEIN COUPLED RECEPTOR | ||||||
Function / homology | Function and homology information granulocyte chemotaxis / chondroitin sulfate binding / regulation of mast cell degranulation / leading edge membrane / Class B/2 (Secretin family receptors) / G protein-coupled receptor activity / ruffle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell migration / cell surface receptor signaling pathway ...granulocyte chemotaxis / chondroitin sulfate binding / regulation of mast cell degranulation / leading edge membrane / Class B/2 (Secretin family receptors) / G protein-coupled receptor activity / ruffle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell migration / cell surface receptor signaling pathway / cell adhesion / inflammatory response / G protein-coupled receptor signaling pathway / calcium ion binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Abbott, R.J.M. / Spendlove, I. / Roversi, P. / Teriete, P. / Knott, V. / Handford, P.A. / McDonnell, J.M. / Lea, S.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural and Functional Characterization of a Novel T Cell Receptor Co-Regulatory Protein Complex, Cd97-Cd55. Authors: Abbott, R.J.M. / Spendlove, I. / Roversi, P. / Fitzgibbon, H. / Knott, V. / Teriete, P. / Mcdonnell, J.M. / Handford, P.A. / Lea, S.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Three Egf Domains of Emr2, a 7Tm Immune-System Molecule Authors: Abbott, R.J.M. / Knott, V. / Roversi, P. / Neudeck, S. / Lukacik, P. / Handford, P.A. / Lea, S.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2box.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2box.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 2box.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2box_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2box_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 2box_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 2box_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2box ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2box | HTTPS FTP |
-Related structure data
Related structure data | 2bo2C 2bouSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15593.094 Da / Num. of mol.: 1 / Fragment: EGF DOMAINS 1,2 AND 5,RESIDUES 25-118,212-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / Variant (production host): PREP4 / References: UniProt: Q9UHX3 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-CAC / | #5: Water | ChemComp-HOH / | Sequence details | THIS PDB DESCIBES THE ALTERNATIV | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.2 % |
---|---|
Crystal grow | pH: 6.5 Details: 0.1 M STRONTIUM CHLORIDE, 12-16% W/V PEG 8000, 0.1 M NA CACODYLATE BUFFER PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→23.26 Å / Num. obs: 8270 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 0.083 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN) Resolution: 2.5→23.262 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO.DAT / Details: REFINED USING BUSTER-TNT VERSION 1.0.4
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET MASKING / Bsol: 30.4 Å2 / ksol: 0.407 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→23.262 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|