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- PDB-6luo: Structure of nurse shark beta-2-microglobulin -

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Basic information

Entry
Database: PDB / ID: 6luo
TitleStructure of nurse shark beta-2-microglobulin
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / nurse shark / monomer beta-2-microglobulin / MHC class I
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / extracellular region
Similarity search - Function
Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsXia, C. / Wu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: J Immunol. / Year: 2021
Title: The Structure of a Peptide-Loaded Shark MHC Class I Molecule Reveals Features of the Binding between beta 2 -Microglobulin and H Chain Conserved in Evolution.
Authors: Wu, Y. / Zhang, N. / Wei, X. / Lu, S. / Li, S. / Hashimoto, K. / Dijkstra, J.M. / Xia, C.
History
DepositionJan 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)22,0792
Polymers22,0792
Non-polymers00
Water2,288127
1
A: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,0391
Polymers11,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,0391
Polymers11,0391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.230, 88.230, 67.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

21A-142-

HOH

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Components

#1: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11039.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Gene: B2M, b2m / Production host: Escherichia coli (E. coli) / References: UniProt: F4ZE04
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 2%(v/v) polyethylene glycol 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2011
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12880 / % possible obs: 93.92 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 33.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 14.6 / Num. unique obs: 949 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KJV

1kjv


Resolution: 2.302→33.228 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.91 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2695 639 4.961 %
Rwork0.2376 --
all0.239 --
obs-12880 93.919 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.185 Å20 Å2
2--0.37 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.302→33.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 0 127 1655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.362500.325949X-RAY DIFFRACTION99.7006
2.362-2.4260.406500.291923X-RAY DIFFRACTION100
2.426-2.4970.27445879X-RAY DIFFRACTION100
2.497-2.5730.319440.291887X-RAY DIFFRACTION100
2.573-2.6580.27748839X-RAY DIFFRACTION100
2.658-2.7510.279420.277832X-RAY DIFFRACTION100
2.751-2.8550.26450786X-RAY DIFFRACTION100
2.855-2.9710.346380.242770X-RAY DIFFRACTION100
2.971-3.1030.293400.234725X-RAY DIFFRACTION99.8695
3.103-3.2540.242420.229703X-RAY DIFFRACTION99.5989
3.254-3.430.312290.218663X-RAY DIFFRACTION99.5683
3.43-3.6370.228260.209559X-RAY DIFFRACTION86.0294
3.637-3.8880.2277259X-RAY DIFFRACTION42.492
3.888-4.1980.204210.197368X-RAY DIFFRACTION65.2685
4.198-4.5980.278280.177487X-RAY DIFFRACTION93.4664
4.598-5.1380.13524444X-RAY DIFFRACTION93.9759
5.138-5.9280.221200.21421X-RAY DIFFRACTION99.3243
5.928-7.250.43140.258366X-RAY DIFFRACTION99.2167

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