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- PDB-4dzb: Mucosal-associated invariant T cell receptor, Valpha7.2Jalpha33-Vbeta2 -

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Basic information

Entry
Database: PDB / ID: 4dzb
TitleMucosal-associated invariant T cell receptor, Valpha7.2Jalpha33-Vbeta2
Components
  • Valpha7.2-Jalpha33 (MAIT T cell receptor)
  • Vbeta2 (MAIT T cell receptor)
KeywordsIMMUNE SYSTEM / MAIT T cell receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2012
Title: Structural insight into MR1-mediated recognition of the mucosal associated invariant T cell receptor.
Authors: Reantragoon, R. / Kjer-Nielsen, L. / Patel, O. / Chen, Z. / Illing, P.T. / Bhati, M. / Kostenko, L. / Bharadwaj, M. / Meehan, B. / Hansen, T.H. / Godfrey, D.I. / Rossjohn, J. / McCluskey, J.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Sep 13, 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Valpha7.2-Jalpha33 (MAIT T cell receptor)
B: Vbeta2 (MAIT T cell receptor)


Theoretical massNumber of molelcules
Total (without water)50,3232
Polymers50,3232
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-27 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.962, 64.515, 155.120
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: Protein Valpha7.2-Jalpha33 (MAIT T cell receptor) / Mucosal-associated invariant T cell receptor


Mass: 22700.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b / Production host: Escherichia coli (E. coli)
#2: Protein Vbeta2 (MAIT T cell receptor)


Mass: 27622.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% PEG 1500, 0.1M MIB buffer (sodium malonate, imidazole, boric acid), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 45957 / Num. obs: 44624 / % possible obs: 97.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6281 / % possible all: 92.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NX5

2nx5


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.115 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23063 2325 5.1 %RANDOM
Rwork0.19067 ---
obs0.19264 43627 96.97 %-
all-44990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 271 3695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223583
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9314900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38724.94166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65215564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0611512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212773
X-RAY DIFFRACTIONr_mcbond_it0.9811.52236
X-RAY DIFFRACTIONr_mcangle_it1.7523624
X-RAY DIFFRACTIONr_scbond_it2.59531347
X-RAY DIFFRACTIONr_scangle_it4.1844.51262
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 171 -
Rwork0.276 3012 -
obs-3183 92.13 %

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