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- PDB-6k7u: Crystal structure of beta-2 microglobulin (beta2m) of Bat (Pterop... -

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Basic information

Entry
Database: PDB / ID: 6k7u
TitleCrystal structure of beta-2 microglobulin (beta2m) of Bat (Pteropus Alecto)
ComponentsBat beta-2-microglobulin
KeywordsIMMUNE SYSTEM / Immune molecular
Function / homology
Function and homology information


response to metal ion / 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 ...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 / Nucleic acid-binding, OB-fold / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsLu, D. / Liu, K.F. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Chai, Y. / Qi, J.X. / Gao, F.G. / Liu, W.J.
CitationJournal: Plos Biol. / Year: 2019
Title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.
Authors: Lu, D. / Liu, K. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Wang, L. / Chai, Y. / Qi, J. / Wang, L.F. / Gao, G.F. / Liu, W.J.
History
DepositionJun 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 4, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
B: Bat beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,5761
Polymers11,5761
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6370 Å2
Unit cell
Length a, b, c (Å)33.707, 114.641, 57.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-176-

HOH

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Components

#1: Protein Bat beta-2-microglobulin


Mass: 11575.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: L5K3Y9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 8% w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: SDMS / Detector: OSCILLATION CAMERA / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 15045 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 28.036
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 15045

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→40.527 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.2022 713 4.79 %
Rwork0.1954 --
obs0.1958 14900 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→40.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 0 87 887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006849
X-RAY DIFFRACTIONf_angle_d1.0151159
X-RAY DIFFRACTIONf_dihedral_angle_d26.291319
X-RAY DIFFRACTIONf_chiral_restr0.086117
X-RAY DIFFRACTIONf_plane_restr0.007153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6006-1.72410.30121480.25282635X-RAY DIFFRACTION94
1.7241-1.89760.23691460.22092808X-RAY DIFFRACTION100
1.8976-2.17220.21321360.19162861X-RAY DIFFRACTION100
2.1722-2.73670.22151420.21222872X-RAY DIFFRACTION100
2.7367-40.53990.16191410.1723011X-RAY DIFFRACTION100

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