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- PDB-8k8h: Crystal structure of the CysR-CTLD3 fragment of human DEC205 -

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Basic information

Entry
Database: PDB / ID: 8k8h
TitleCrystal structure of the CysR-CTLD3 fragment of human DEC205
ComponentsLymphocyte antigen 75
KeywordsRECOMBINATION / DEC 205 / CD205 / Keratin / Dead cell / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsQian, Y. / Kong, D. / Yu, B. / He, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 91957102 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Interaction of human dendritic cell receptor DEC205/CD205 with keratins.
Authors: Kong, D. / Qian, Y. / Yu, B. / Hu, Z. / Cheng, C. / Wang, Y. / Fang, Z. / Yu, J. / Xiang, S. / Cao, L. / He, Y.
History
DepositionJul 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lymphocyte antigen 75


Theoretical massNumber of molelcules
Total (without water)68,3121
Polymers68,3121
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.582, 79.205, 89.542
Angle α, β, γ (deg.)90.00, 121.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lymphocyte antigen 75


Mass: 68312.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LY75, CD205, CLEC13B / Production host: Trichoplusia ni (cabbage looper)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M Sodium Citrate, 20% PEG3350, final pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→29.64 Å / Num. obs: 21098 / % possible obs: 99.41 % / Redundancy: 3.3 % / Rpim(I) all: 0.073 / Net I/σ(I): 13.3
Reflection shellResolution: 2.79→2.86 Å / Num. unique obs: 2214 / Rpim(I) all: 0.153

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT4.1data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6INN

6inn


Resolution: 2.79→29.64 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1983 9.46 %
Rwork0.1906 --
obs0.1977 20954 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 0 67 4694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.091
X-RAY DIFFRACTIONf_dihedral_angle_d7.227615
X-RAY DIFFRACTIONf_chiral_restr0.059659
X-RAY DIFFRACTIONf_plane_restr0.008830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.860.34431290.26081227X-RAY DIFFRACTION92
2.86-2.940.34121400.2481350X-RAY DIFFRACTION100
2.94-3.030.35531400.24331360X-RAY DIFFRACTION100
3.03-3.120.29741440.2541352X-RAY DIFFRACTION100
3.12-3.240.32481370.24941360X-RAY DIFFRACTION100
3.24-3.370.33691480.22661358X-RAY DIFFRACTION100
3.37-3.520.30931370.21151358X-RAY DIFFRACTION100
3.52-3.70.26411410.1871358X-RAY DIFFRACTION100
3.7-3.940.25491430.17921360X-RAY DIFFRACTION100
3.94-4.240.2431470.16291367X-RAY DIFFRACTION100
4.24-4.660.2221360.14951369X-RAY DIFFRACTION100
4.66-5.330.22731480.15041364X-RAY DIFFRACTION100
5.33-6.710.23991450.17351381X-RAY DIFFRACTION100
6.71-29.640.22351480.18631407X-RAY DIFFRACTION100

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