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- PDB-5mix: Extracellular domain of human CD83 - trigonal crystal form -

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Basic information

Entry
Database: PDB / ID: 5mix
TitleExtracellular domain of human CD83 - trigonal 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 / humoral immune response / positive regulation of interleukin-10 production / positive regulation of interleukin-2 production / 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: 1.701 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD83 antigen


Theoretical massNumber of molelcules
Total (without water)12,7671
Polymers12,7671
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.942, 62.942, 40.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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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.: 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 remains after the GST-tag was cleaved off. The first three and last four residues as well as the central region ...Details: The first four residues (GSPG) are non-native residues of the linker which remains after the GST-tag was cleaved off. The first three and last four 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(DE3) (bacteria) / Variant (production host): Gold pLysS / References: UniProt: Q01151
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.79 Å3/Da / Density % sol: 31.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4 microliter protein (39 mg/ml in 50 mM Tris-HCl (pH 8.0) buffer) were mixed with 0.2 microliter reservoir solution (1 M ammonium sulfate, 0.1 M HEPES (pH 7.0), 0.5% w/v polyethylene ...Details: 0.4 microliter protein (39 mg/ml in 50 mM Tris-HCl (pH 8.0) buffer) were mixed with 0.2 microliter reservoir solution (1 M ammonium sulfate, 0.1 M HEPES (pH 7.0), 0.5% w/v polyethylene glycol (PEG) 8000) and equilibrated against 70 microliter of reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.7→40.06 Å / Num. obs: 10348 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
RefinementResolution: 1.701→40.06 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2164 1026 9.92 %
Rwork0.1884 --
obs0.1912 10347 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.6 Å2
Refinement stepCycle: LAST / Resolution: 1.701→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms597 0 0 31 628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006663
X-RAY DIFFRACTIONf_angle_d1.088914
X-RAY DIFFRACTIONf_dihedral_angle_d12.682252
X-RAY DIFFRACTIONf_chiral_restr0.049106
X-RAY DIFFRACTIONf_plane_restr0.006121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.79030.32181440.27861290X-RAY DIFFRACTION100
1.7903-1.90250.23451460.21431319X-RAY DIFFRACTION100
1.9025-2.04940.26511460.18551307X-RAY DIFFRACTION100
2.0494-2.25560.19631470.1931333X-RAY DIFFRACTION100
2.2556-2.58190.23361440.20071316X-RAY DIFFRACTION100
2.5819-3.25270.24041470.21171349X-RAY DIFFRACTION100
3.2527-40.07510.19251520.16811407X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9805-3.26960.26313.75320.89690.7719-0.2623-2.2640.9623-0.1892-0.12420.3508-0.8455-2.28950.34510.37750.0767-0.01290.5567-0.02190.311791.79683.164658.0915
21.26552.05160.9494.8791-1.37456.1948-0.1144-0.7926-1.84210.33870.60520.34470.3446-0.6172-0.35680.3542-0.0882-0.09360.27150.05970.877990.304970.67954.8268
39.05965.3011-2.51493.5764-1.89076.8041-0.34980.7888-1.0635-1.5850.4434-0.59320.5499-0.1007-0.06860.35880.0109-0.080.3435-0.06190.352396.784175.587349.6133
45.0475-2.7898-4.74037.51513.29845.30310.09770.71670.4581-0.8002-0.05490.0458-0.5068-0.3868-0.01370.5921-0.01970.08250.47060.01720.3381105.939489.344443.8169
58.6365-0.71560.23038.0838-0.28361.7446-0.08650.00150.0423-0.00190.1735-0.0444-0.2217-0.0718-0.11220.21030.01990.03470.2553-0.02440.2015105.215678.935557.6473
69.4373.8303-1.78074.0413-3.72815.5039-0.39851.2694-0.7416-1.44460.6545-0.5690.0564-0.5835-0.1720.48190.021-0.01710.4256-0.05640.2086100.872678.434846.2961
75.15371.4737-3.70778.9273-0.16272.8945-0.59790.0333-1.9754-1.0073-0.03040.09541.41840.62420.39160.66040.0239-0.05050.3701-0.00340.768197.618966.141554.5096
86.72913.2858-3.68016.4826-3.69546.4420.3834-0.1933-0.0826-0.0381-0.3727-0.7463-0.35560.6084-0.01970.28350.03620.07080.2988-0.00730.2446106.550683.602452.9031
93.67071.5224-5.60393.9815-3.00827.74630.4857-0.1506-0.33720.1035-0.224-0.7909-0.36460.4999-0.29760.2720.02960.0490.2807-0.00410.3194106.467589.001353.4173
102.37641.87352.42224.53624.83145.3838-0.1122-0.9525-0.84151.1134-0.52541.62270.5544-2.0150.14320.4680.01490.01170.48340.07770.458891.630272.787358.8438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 19:22)
2X-RAY DIFFRACTION2(chain A and resid 23:27)
3X-RAY DIFFRACTION3(chain A and resid 28:36)
4X-RAY DIFFRACTION4(chain A and resid 37:47)
5X-RAY DIFFRACTION5(chain A and resid 48:87)
6X-RAY DIFFRACTION6(chain A and resid 88:94)
7X-RAY DIFFRACTION7(chain A and resid 95:100)
8X-RAY DIFFRACTION8(chain A and resid 101:114)
9X-RAY DIFFRACTION9(chain A and resid 115:123)
10X-RAY DIFFRACTION10(chain A and resid 124:127)

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