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- PDB-3axl: Murine Valpha 10 Vbeta 8.1 T-cell receptor -

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Basic information

Entry
Database: PDB / ID: 3axl
TitleMurine Valpha 10 Vbeta 8.1 T-cell receptor
Components
  • Valpha 10
  • Vbeta 8.1
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / T-cell receptor / CD1d binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2011
Title: A semi-invariant V(alpha)10(+) T cell antigen receptor defines a population of natural killer T cells with distinct glycolipid antigen-recognition properties
Authors: Uldrich, A.P. / Patel, O. / Cameron, G. / Pellicci, D.G. / Day, E.B. / Sullivan, L.C. / Kyparissoudis, K. / Kjer-Nielsen, L. / Vivian, J.P. / Cao, B. / Brooks, A.G. / Williams, S.J. / ...Authors: Uldrich, A.P. / Patel, O. / Cameron, G. / Pellicci, D.G. / Day, E.B. / Sullivan, L.C. / Kyparissoudis, K. / Kjer-Nielsen, L. / Vivian, J.P. / Cao, B. / Brooks, A.G. / Williams, S.J. / Illarionov, P. / Besra, G.S. / Turner, S.J. / Porcelli, S.A. / McCluskey, J. / Smyth, M.J. / Rossjohn, J. / Godfrey, D.I.
History
DepositionApr 11, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Valpha 10
B: Vbeta 8.1
G: Valpha 10
H: Vbeta 8.1


Theoretical massNumber of molelcules
Total (without water)97,0014
Polymers97,0014
Non-polymers00
Water2,306128
1
A: Valpha 10
B: Vbeta 8.1


Theoretical massNumber of molelcules
Total (without water)48,5012
Polymers48,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-22 kcal/mol
Surface area20140 Å2
MethodPISA
2
G: Valpha 10
H: Vbeta 8.1


Theoretical massNumber of molelcules
Total (without water)48,5012
Polymers48,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-22 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.841, 65.801, 97.375
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21H
12A
22G

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAARGARGchain B and (resseq 3:240 )BB3 - 2401 - 222
211ALAALAARGARGchain H and (resseq 3:240 )HD3 - 2401 - 222
112GLNGLNGLYGLYchain A and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )AA3 - 481 - 39
122LEULEUGLYGLYchain A and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )AA54 - 6445 - 55
132GLYGLYLEULEUchain A and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )AA70 - 12456 - 104
142ASNASNALAALAchain A and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )AA132 - 200112 - 180
212GLNGLNGLYGLYchain G and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )GC3 - 481 - 39
222LEULEUGLYGLYchain G and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )GC54 - 6445 - 55
232GLYGLYLEULEUchain G and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )GC70 - 12456 - 104
242ASNASNALAALAchain G and (resseq 3:48 or resseq 54:64 or resseq 70:124 or resseq 132:200 )GC132 - 200112 - 180

NCS ensembles :
ID
1
2

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Components

#1: Antibody Valpha 10


Mass: 21657.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Protein Vbeta 8.1


Mass: 26842.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 49.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M NaI, 0.1M Bis-Tris-Propane, pH 6.5, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20901 / Num. obs: 20901 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→42.945 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7143 / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1029 5.09 %Random
Rwork0.2536 ---
obs0.2575 20217 96.36 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.924 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 130.16 Å2 / Biso mean: 34.389 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--4.0864 Å20 Å2-0.4506 Å2
2--5.9053 Å20 Å2
3----6.4244 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 0 128 6728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156971
X-RAY DIFFRACTIONf_angle_d1.689189
X-RAY DIFFRACTIONf_chiral_restr0.1171009
X-RAY DIFFRACTIONf_plane_restr0.0091200
X-RAY DIFFRACTIONf_dihedral_angle_d16.5972403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1883X-RAY DIFFRACTIONPOSITIONAL0.071
12H1883X-RAY DIFFRACTIONPOSITIONAL0.071
21A1393X-RAY DIFFRACTIONPOSITIONAL0.065
22G1393X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.05290.35931350.29522516265190
3.0529-3.24410.39031430.28632673281694
3.2441-3.49450.35141320.27452733286597
3.4945-3.8460.35381370.25822800293798
3.846-4.4020.33261530.23242785293898
4.402-5.54420.271670.22062799296699
5.5442-42.950.30251620.25822882304498

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