+Open data
-Basic information
Entry | Database: PDB / ID: 1e8i | ||||||
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Title | HUMAN CD69 - TETRAGONAL FORM | ||||||
Components | EARLY ACTIVATION ANTIGEN CD69 | ||||||
Keywords | HEMATOPOIETIC CELL RECEPTOR / LEUCOCYTE / C-TYPE LECTIN-LIKE / NKD / KLR | ||||||
Function / homology | Function and homology information transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / carbohydrate binding / external side of plasma membrane / protein-containing complex / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Tormo, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal Structure of the C-Type Lectin-Like Domain from the Human Hematopoietic Cell Receptor Cd69 Authors: Llera, A.S. / Viedma, F. / Sanchez-Madrid, F. / Tormo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e8i.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e8i.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e8i ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e8i | HTTPS FTP |
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-Related structure data
Related structure data | 1e87C 1b6eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9721, -0.21762, -0.08752), Vector: |
-Components
#1: Protein | Mass: 13806.557 Da / Num. of mol.: 2 / Fragment: C-TYPE LECTIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: HEMATOPOIETIC CELL / Cellular location: CELL SURFACECell membrane / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07108 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Compound details | SIGNAL TRANSMITTING RECEPTOR IN LYMPHOCYTES, NATURAL KILLER (NK) CELLS, AND PLATELETS. INVOLVED IN ...SIGNAL TRANSMITTI | |
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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: 2.6 Å3/Da / Density % sol: 51 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: pH 4.80 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusionDetails: drop consists of equal amounts of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 21836 / % possible obs: 99.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.256 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 98431 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B6E Resolution: 1.95→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.4589 Å2 / ksol: 0.352836 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 19826 / % reflection Rfree: 9.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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