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Yorodumi- PDB-2ja4: Crystal structure of CD5 domain III reveals the fold of a group B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ja4 | ||||||
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Title | Crystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor | ||||||
Components | T-CELL SURFACE GLYCOPROTEIN CD5 | ||||||
Keywords | IMMUNE SYSTEM / CD6 / CD5 / SRCR / MEMBRANE / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / INNATE IMMUNITY / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information cell recognition / T cell costimulation / apoptotic signaling pathway / signaling receptor activity / external side of plasma membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å | ||||||
Authors | Rodamilans, B. / Munoz, I.G. / Sarrias, M.R. / Lozano, F. / Blanco, F.J. / Montoya, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of the Third Extracellular Domain of Cd5 Reveals the Fold of a Group B Scavenger Cysteine-Rich Receptor Domain. Authors: Rodamilans, B. / Munoz, I.G. / Bragado-Nilsson, E. / Sarrias, M.R. / Padilla, O. / Blanco, F.J. / Lozano, F. / Montoya, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ja4.cif.gz | 29.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ja4.ent.gz | 22.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ja4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ja4_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 2ja4_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 2ja4_validation.xml.gz | 7 KB | Display | |
Data in CIF | 2ja4_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2ja4 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2ja4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11315.667 Da / Num. of mol.: 1 / Fragment: DOMAIN III, RESIDUES 269-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Plasmid: PCEP-PU / Cell line (production host): HEK-293EBNA / Production host: HOMO SAPIENS (human) / Tissue (production host): KIDNEY CELLS / References: UniProt: P06127 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | pH: 7.4 / Details: 15-25% PEG 8000, 100 MM NAAC PH 4.4, 200 MM LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.8 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 12098 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.21→2.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.21→19.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.474 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→19.18 Å
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Refine LS restraints |
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