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- PDB-5mj0: Extracellular domain of human CD83 - cubic crystal form -

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Basic information

Entry
Database: PDB / ID: 5mj0
TitleExtracellular domain of human CD83 - cubic crystal form
ComponentsCD83 antigen
KeywordsIMMUNE 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
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsKlingl, S. / Egerer-Sieber, C. / Schmid, B. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: 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
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD83 antigen
B: CD83 antigen


Theoretical massNumber of molelcules
Total (without water)25,5342
Polymers25,5342
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.564, 149.564, 149.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein CD83 antigen / hCD83 / B-cell activation protein / Cell surface protein HB15


Mass: 12766.979 Da / Num. of mol.: 2 / 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 remains after the GST-tag was cleaved off. The first and last two residues as well as the central region were not ...Details: The first four residues (GSPG) are non-native residues of the linker which remains after the GST-tag was cleaved off. 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 microliter protein (21 mg/ml in 25 mM Tris-HCl (pH 7.2) buffer) were mixed with 0.2 microliter reservoir solution (0.2 M L-proline, 0.1 M HEPES (pH 7.5), 24% w/v PEG 1500) and ...Details: 0.2 microliter protein (21 mg/ml in 25 mM Tris-HCl (pH 7.2) buffer) were mixed with 0.2 microliter reservoir solution (0.2 M L-proline, 0.1 M HEPES (pH 7.5), 24% w/v PEG 1500) and equilibrated against 70 microliter of reservoir solution Crystals appeared after ~ 10 months

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918007 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918007 Å / Relative weight: 1
ReflectionResolution: 3.2→47.3 Å / Num. obs: 4984 / % possible obs: 99.7 % / Redundancy: 12.6 % / Biso Wilson estimate: 103.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.9
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 13 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
RefinementResolution: 3.2→47.296 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.83
RfactorNum. reflection% reflection
Rfree0.2636 250 5.02 %
Rwork0.2373 --
obs0.2388 4982 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→47.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 0 1222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061250
X-RAY DIFFRACTIONf_angle_d1.3451705
X-RAY DIFFRACTIONf_dihedral_angle_d13.733468
X-RAY DIFFRACTIONf_chiral_restr0.053199
X-RAY DIFFRACTIONf_plane_restr0.007218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1974-4.02810.34191220.31152302X-RAY DIFFRACTION100
4.0281-47.30140.24361280.21792430X-RAY DIFFRACTION100

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