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- PDB-1bmg: CRYSTAL STRUCTURE OF BOVINE BETA2-MICROGLOBULIN -

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Basic information

Entry
Database: PDB / ID: 1bmg
TitleCRYSTAL STRUCTURE OF BOVINE BETA2-MICROGLOBULIN
ComponentsBETA=2=-MICROGLOBULIN
KeywordsHISTOCOMPATIBILITY ANTIGEN / LACTOLLIN / MHC-I HISTOCOMPATIBILITY ANTIGEN / LIGHT CHAIN
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBecker, J.W. / Reeke Junior, G.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Three-dimensional structure of beta 2-microglobulin.
Authors: Becker, J.W. / Reeke Jr., G.N.
#1: Journal: J.Biol.Chem. / Year: 1982
Title: Complete Amino Acid Sequence of Bovine Beta2-Microglobulin
Authors: Groves, M.L. / Greenberg, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Crystallographic Studies of Bovine Beta2-Microglobulin
Authors: Becker, J.W. / Ziffer, J.A. / Edelman, G.M. / Cunningham, B.A.
History
DepositionJul 18, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Nov 20, 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
Remark 700SHEET ONE OF THE TWO BETA-SHEETS OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE ...SHEET ONE OF THE TWO BETA-SHEETS OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3 OF S1 AND S2 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA=2=-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)11,6531
Polymers11,6531
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.270, 47.990, 34.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 32

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Components

#1: Protein BETA=2=-MICROGLOBULIN


Mass: 11653.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell line: S2 / Tissue: MILK, COLOSTRUM / References: UniProt: P01888
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal grow
*PLUS
Method: microdialysis
Details: Becker, J.W., (1977) Proc. Natl. Acad. Sci. U.S.A., 74, 3345.
PH range low: 8.5 / PH range high: 7
Components of the solutions
*PLUS
Conc.: 0.05-0.005 M / Common name: sodium phosphate

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: FILM / Date: 1985
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→48 Å / Num. obs: 3960 / % possible obs: 65 % / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Rmerge(I) obs: 0.0943
Reflection
*PLUS
Rmerge(I) obs: 0.0943

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
X-PLOR3.1model building
PROLSQrefinement
ROCKSdata collection
X-PLOR3.1phasing
RefinementResolution: 2.5→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.29 --
Rwork0.1914 --
obs0.1914 3177 69.3 %
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 72 1086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2909
Solvent computation
*PLUS
Displacement parameters
*PLUS

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