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- PDB-3o81: Beta2-microglobulin from Gallus gallus -

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Basic information

Entry
Database: PDB / ID: 3o81
TitleBeta2-microglobulin from Gallus gallus
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Ig-like C1-type (immunoglobulin-like) domain / HISTOCOMPATIBILITY ANTIGEN / MHC class I molecule from B21 chicken
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLoll, B. / Hee, C.S. / Uchanska-Ziegler, B. / Ziegler, A.
CitationJournal: Biophys.Chem. / Year: 2012
Title: Comparative biophysical characterization of chicken beta2-microglobulin.
Authors: Hee, C.S. / Fabian, H. / Uchanska-Ziegler, B. / Ziegler, A. / Loll, B.
History
DepositionAug 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,1102
Polymers26,1102
Non-polymers00
Water2,882160
1
A: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)13,0551
Polymers13,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)13,0551
Polymers13,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-9 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.920, 30.480, 87.360
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-2-microglobulin


Mass: 13054.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Plasmid: pMAL-p4x / Production host: Escherichia coli (E. coli) / Strain (production host): TB1 / References: UniProt: P21611
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22%(w/v) PEG 3350, 200mM Mg2Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→36.85 Å / Num. all: 13485 / Num. obs: 12952 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.088 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 1671 / Rsym value: 0.193 / % possible all: 92.2

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Processing

Software
NameVersionClassification
MAR345softwaredata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BEW

3bew


Resolution: 2→36.85 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.825 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24189 667 5 %RANDOM
Rwork0.19493 ---
obs0.19723 12672 100 %-
all-13485 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å21.37 Å2
2---0.7 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 0 160 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221674
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9372304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57924.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94815269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.1154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211312
X-RAY DIFFRACTIONr_mcbond_it0.5771.51019
X-RAY DIFFRACTIONr_mcangle_it1.08721672
X-RAY DIFFRACTIONr_scbond_it1.6163655
X-RAY DIFFRACTIONr_scangle_it2.5644.5617
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 48 -
Rwork0.193 924 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43920.0873-1.26292.0147-0.01292.6452-0.01940.0543-0.01350.05710.03790.1343-0.0229-0.1715-0.01840.00330.0019-0.00060.02860.00180.04199.7627-7.62592.4487
22.0555-0.26471.3322.67930.24273.5443-0.0321-0.07940.0523-0.09620.0610.1370.0367-0.2669-0.02890.0148-0.00910.00750.04420.00530.0437.04910.032341.1402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 97
2X-RAY DIFFRACTION2B1 - 97

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