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- PDB-5xs3: Crystal structure of HLA Class I antigen -

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Basic information

Entry
Database: PDB / ID: 5xs3
TitleCrystal structure of HLA Class I antigen
Components
  • Heavy Chain
  • Light Chain
  • P
KeywordsIMMUNE SYSTEM / HLA Class I antigen
Function / homologyMHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWei, P.C. / Yang, Y. / Liu, Z.X. / Luo, Z.Q. / Tu, W.Y. / Han, J.Y. / Deng, Y.H. / Yin, L.
CitationJournal: J. Invest. Dermatol. / Year: 2017
Title: Characterization of Autoantigen Presentation by HLA-C*06:02 in Psoriasis
Authors: Wei, P. / Yang, Y. / Liu, Z. / Luo, Z. / Tu, W. / Han, J. / Deng, Y. / Yin, L.
History
DepositionJun 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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: Heavy Chain
B: Light Chain
C: P


Theoretical massNumber of molelcules
Total (without water)44,5113
Polymers44,5113
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-14 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.210, 81.100, 117.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy Chain


Mass: 31785.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Light Chain


Mass: 11562.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide P


Mass: 1162.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.2M Ammonium chloride, 0.1M MES pH 6.0, 20%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 13478 / % possible obs: 89 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.08364 / Net I/σ(I): 6.96
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.62 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQD

1qqd


Resolution: 2.5→40 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.97
RfactorNum. reflection% reflection
Rfree0.2724 1348 10 %
Rwork0.2143 --
obs0.2202 13477 88.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 0 120 3134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053097
X-RAY DIFFRACTIONf_angle_d0.7894221
X-RAY DIFFRACTIONf_dihedral_angle_d16.7161815
X-RAY DIFFRACTIONf_chiral_restr0.045436
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.38311360.26131221X-RAY DIFFRACTION92
2.5894-2.6930.27561350.26151213X-RAY DIFFRACTION91
2.693-2.81560.29891360.24671236X-RAY DIFFRACTION91
2.8156-2.9640.31861360.25131215X-RAY DIFFRACTION91
2.964-3.14960.31931350.22921220X-RAY DIFFRACTION90
3.1496-3.39270.291350.20251209X-RAY DIFFRACTION89
3.3927-3.73390.24991330.19051198X-RAY DIFFRACTION89
3.7339-4.27370.25991330.1841200X-RAY DIFFRACTION87
4.2737-5.38260.20551330.17731196X-RAY DIFFRACTION86
5.3826-41.37010.2321360.22421222X-RAY DIFFRACTION83
Refinement TLS params.Method: refined / Origin x: 8.5719 Å / Origin y: 85.6046 Å / Origin z: 14.3364 Å
111213212223313233
T0.0524 Å20.0078 Å2-0.0131 Å2-0.0717 Å20.021 Å2--0.0714 Å2
L0.3707 °2-0.1897 °2-0.212 °2-0.7408 °20.4111 °2--0.6371 °2
S0.0168 Å °0.048 Å °-0.0357 Å °-0.0369 Å °-0.0459 Å °0.0364 Å °-0.0663 Å °-0.0506 Å °-0.2299 Å °
Refinement TLS groupSelection details: all

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