+Open data
-Basic information
Entry | Database: PDB / ID: 5mj1 | ||||||
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Title | Extracellular domain of human CD83 - rhombohedral crystal form | ||||||
Components | CD83 antigen | ||||||
Keywords | IMMUNE SYSTEM / Dendritic cell / receptor / immunoglobulin | ||||||
Function / homology | Function and homology information positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of interleukin-4 production / CD4-positive, alpha-beta T cell differentiation / positive regulation of interleukin-10 production / humoral immune response / positive regulation of interleukin-2 production / response to organic cyclic compound / defense response / external side of plasma membrane / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Klingl, S. / Egerer-Sieber, C. / Schmid, B. / Weiler, S. / Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Crystal Structure of the Extracellular Domain of the Human Dendritic Cell Surface Marker CD83. Authors: Heilingloh, C.S. / Klingl, S. / Egerer-Sieber, C. / Schmid, B. / Weiler, S. / Muhl-Zurbes, P. / Hofmann, J. / Stump, J.D. / Sticht, H. / Kummer, M. / Steinkasserer, A. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mj1.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mj1.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mj1 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mj1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12766.979 Da / Num. of mol.: 1 / Mutation: C27S, C100S, C129S Source method: isolated from a genetically manipulated source Details: The first four residues (GSPG) are non-native residues of the linker which remain after the GST-tag was cleaved off. The third residue (P) was modeled as alanine due to missing electron ...Details: The first four residues (GSPG) are non-native residues of the linker which remain after the GST-tag was cleaved off. The third residue (P) was modeled as alanine due to missing electron density. The first and last two residues as well as the central region were not visible in the electron density maps. Source: (gene. exp.) Homo sapiens (human) / Cell: Dendritic cells / Gene: CD83 / Plasmid: pGEX-2T / Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q01151 |
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#2: Chemical | ChemComp-PEG / |
#3: 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: 2 Å3/Da / Density % sol: 38.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 microliter protein (39 mg/ml in ultrapure water) mixed with 0.4 microliter reservoir solution (0.2 M DL-malic acid (pH 7.0), 20% w/v PEG 3350) was equilibrated against 70 microliter of ...Details: 0.2 microliter protein (39 mg/ml in ultrapure water) mixed with 0.4 microliter reservoir solution (0.2 M DL-malic acid (pH 7.0), 20% w/v PEG 3350) was equilibrated against 70 microliter of reservoir solution. Crystals appeared after ~ 13 months |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.4 Å / Num. obs: 9772 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.4 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.4 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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