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- PDB-6lir: crystal structure of chicken TCR for 2.0 -

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Basic information

Entry
Database: PDB / ID: 6lir
Titlecrystal structure of chicken TCR for 2.0
Components
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / TCR / Chicken
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.091 Å
AuthorsZhang, L. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972683 China
National Natural Science Foundation of China (NSFC)31572493 China
CitationJournal: Iscience / Year: 2020
Title: Structural and Biophysical Insights into the TCR alpha beta Complex in Chickens.
Authors: Zhang, L. / Liu, Y. / Meng, G. / Liang, R. / Zhang, B. / Xia, C.
History
DepositionDec 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCR alpha chain
B: TCR beta chain
C: TCR alpha chain
D: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)101,1774
Polymers101,1774
Non-polymers00
Water5,405300
1
A: TCR alpha chain
B: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,5882
Polymers50,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-13 kcal/mol
Surface area19690 Å2
MethodPISA
2
C: TCR alpha chain
D: TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,5882
Polymers50,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-12 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.430, 83.097, 82.416
Angle α, β, γ (deg.)90.000, 117.716, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TCR alpha chain


Mass: 23717.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TCR alpha chain / Production host: Escherichia coli (E. coli)
#2: Protein TCR beta chain


Mass: 26871.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25M Lithium citrate tribasic tetrahydrate 24%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.091→50 Å / Num. obs: 54200 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 15.1
Reflection shellResolution: 2.091→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.263 / Num. unique obs: 52151 / Rsym value: 0.86 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.091→38.744 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.008 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2359 2731 5.043 %
Rwork0.2046 --
all0.206 --
obs-54149 98.857 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.724 Å2
Baniso -1Baniso -2Baniso -3
1--1.368 Å20 Å2-0.175 Å2
2--4.275 Å20 Å2
3----1.755 Å2
Refinement stepCycle: LAST / Resolution: 2.091→38.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 0 0 300 6796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1450.3041780.2713453X-RAY DIFFRACTION90.8659
2.145-2.2040.2912430.2493663X-RAY DIFFRACTION98.9612
2.204-2.2680.3141930.2433581X-RAY DIFFRACTION99.0551
2.268-2.3380.2661630.2443507X-RAY DIFFRACTION99.1892
2.338-2.4140.2651520.2513438X-RAY DIFFRACTION99.3359
2.414-2.4990.32050.2513291X-RAY DIFFRACTION99.4595
2.499-2.5930.3021820.2423141X-RAY DIFFRACTION99.2829
2.593-2.6990.2721590.2333044X-RAY DIFFRACTION99.6888
2.699-2.8190.2971450.2312949X-RAY DIFFRACTION99.8064
2.819-2.9560.2681730.232800X-RAY DIFFRACTION99.6648
2.956-3.1160.2541260.2192685X-RAY DIFFRACTION99.8579
3.116-3.3040.2541200.2142560X-RAY DIFFRACTION99.851
3.304-3.5320.2241330.1962384X-RAY DIFFRACTION99.8017
3.532-3.8140.2151220.22221X-RAY DIFFRACTION99.9147
3.814-4.1770.2121140.1782065X-RAY DIFFRACTION99.9541
4.177-4.6680.153710.1521868X-RAY DIFFRACTION99.6403
4.668-5.3870.204750.1611663X-RAY DIFFRACTION99.9425
5.387-6.5880.242580.2121409X-RAY DIFFRACTION99.2558
6.588-9.280.197820.191087X-RAY DIFFRACTION100

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