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Yorodumi- PDB-1ccz: CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ccz | ||||||
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Title | CRYSTAL STRUCTURE OF THE CD2-BINDING DOMAIN OF CD58 (LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 3) AT 1.8-A RESOLUTION | ||||||
Components | PROTEIN (CD58) | ||||||
Keywords | GLYCOPROTEIN / CD58 / LFA-3 | ||||||
Function / homology | Function and homology information heterotypic cell-cell adhesion / ficolin-1-rich granule membrane / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to type II interferon / cellular response to tumor necrosis factor / signaling receptor binding / Neutrophil degranulation ...heterotypic cell-cell adhesion / ficolin-1-rich granule membrane / secretory granule membrane / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to type II interferon / cellular response to tumor necrosis factor / signaling receptor binding / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ikemizu, S. / Sparks, L.M. / Van Der Merwe, P.A. / Harlos, K. / Stuart, D.I. / Jones, E.Y. / Davis, S.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Crystal structure of the CD2-binding domain of CD58 (lymphocyte function-associated antigen 3) at 1.8-A resolution. Authors: Ikemizu, S. / Sparks, L.M. / van der Merwe, P.A. / Harlos, K. / Stuart, D.I. / Jones, E.Y. / Davis, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ccz.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ccz.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ccz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1ccz ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1ccz | HTTPS FTP |
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-Related structure data
Related structure data | 1hngS 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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-Components
#1: Protein | Mass: 19937.602 Da / Num. of mol.: 1 / Fragment: CD2-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19256 | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.7 % | |||||||||||||||
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Crystal grow | pH: 4.6 / Details: 0.1M SODIUM ACETATE PH 4.6, 2.0 M SODIUM CHLORIDE | |||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: unpublished | |||||||||||||||
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: BM14 / Wavelength: 0.8983,0.946 | |||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1997 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. obs: 187375 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9 | |||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.3 / % possible all: 100 | |||||||||
Reflection | *PLUS Num. obs: 37412 / Num. measured all: 187375 | |||||||||
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNG Resolution: 1.8→15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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