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- PDB-5wjo: Crystal structure of the unliganded PG90 TCR -

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Basic information

Entry
Database: PDB / ID: 5wjo
TitleCrystal structure of the unliganded PG90 TCR
Components
  • PG90 TCR alpha chain
  • PG90 TCR beta chain
KeywordsIMMUNE SYSTEM / T Cell Receptor / heterodimer.
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShahine, A. / Gras, S. / Rossjohn, J.
CitationJournal: Sci Immunol / Year: 2017
Title: A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.
Authors: Shahine, A. / Van Rhijn, I. / Cheng, T.Y. / Iwany, S. / Gras, S. / Moody, D.B. / Rossjohn, J.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: PG90 TCR alpha chain
B: PG90 TCR beta chain
C: PG90 TCR alpha chain
D: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89920
Polymers101,2624
Non-polymers63616
Water6,503361
1
A: PG90 TCR alpha chain
B: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,94310
Polymers50,6312
Non-polymers3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-76 kcal/mol
Surface area20580 Å2
MethodPISA
2
C: PG90 TCR alpha chain
D: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95610
Polymers50,6312
Non-polymers3248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-77 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 128.080, 169.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein PG90 TCR alpha chain


Mass: 22839.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Protein PG90 TCR beta chain


Mass: 27791.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

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Non-polymers , 4 types, 377 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.21 Å3/Da / Density % sol: 44.29 % / Description: Single rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 0.2M Magnesium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→39.18 Å / Num. obs: 32046 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.0129 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3558 / CC1/2: 0.607 / Rpim(I) all: 0.0567 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DXA, 1MI5

3dxa

1mi5


Resolution: 2.5→39.18 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.27 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1625 5.07 %RANDOM
Rwork0.208 ---
obs0.209 32046 100 %-
Displacement parametersBiso mean: 37.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.8034 Å20 Å20 Å2
2---3.1822 Å20 Å2
3----1.6212 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.5→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 28 365 7184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077052HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039598HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3194SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes191HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1023HARMONIC5
X-RAY DIFFRACTIONt_it7052HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7814SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.305 130 4.44 %
Rwork0.243 2797 -
all0.246 2927 -
obs--99.97 %
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)
10.5399-0.29210.33790.21690.18240-0.00620.0331-0.04280.0131-0.0087-0.0131-0.0274-0.02890.0149-0.0295-0.03790.0131-0.0026-0.0226-0.015216.895926.9472-40.3168
20.7968-0.24940.220.24620.45580.073-0.02560.00190.0060.0252-0.0048-0.00380.0149-0.0250.0304-0.0025-0.00940.03-0.0197-0.0098-0.028431.17131.3299-27.6182
30.420.0850.03900.29290.59570.011-0.0080.0284-0.0096-0.0005-0.0221-0.01340.0171-0.0104-0.04110.00430.02830.0352-0.043-0.045227.6768-17.5088-6.894
40.19910.08290.12830.31980.20870.23620.02170.00670.0513-0.02310.0150.0113-0.0398-0.0037-0.0367-0.0178-0.01140.0611-0.0047-0.0605-0.001713.5024-4.1105-5.8046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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