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- PDB-6frc: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -

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Basic information

Entry
Database: PDB / ID: 6frc
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(Human T-Cell Receptor ...) x 2
KeywordsIMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 3D Structure
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Front Immunol / Year: 2018
Title: In Silicoand Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility.
Authors: Holland, C.J. / MacLachlan, B.J. / Bianchi, V. / Hesketh, S.J. / Morgan, R. / Vickery, O. / Bulek, A.M. / Fuller, A. / Godkin, A. / Sewell, A.K. / Rizkallah, P.J. / Wells, S. / Cole, D.K.
History
DepositionFeb 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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: Human T-Cell Receptor F11 alpha Chain
B: Human T-Cell Receptor beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18225
Polymers49,6462
Non-polymers1,53623
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint26 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.280, 114.810, 50.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-484-

HOH

31A-541-

HOH

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Components

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Human T-Cell Receptor ... , 2 types, 2 molecules AB

#1: Protein Human T-Cell Receptor F11 alpha Chain


Mass: 22438.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Human T-Cell Receptor beta Chain


Mass: 27208.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 361 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M NaF, 0.1M Bis-Tris Propane, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.59→46.38 Å / Num. obs: 67125 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 22.7
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4908 / CC1/2: 0.824 / Rrim(I) all: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH6

6eh6


Resolution: 1.59→46.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.318 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19751 3398 5.1 %RANDOM
Rwork0.17441 ---
obs0.1756 63670 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.174 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.2 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.59→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 98 338 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193794
X-RAY DIFFRACTIONr_bond_other_d0.0030.023380
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9495132
X-RAY DIFFRACTIONr_angle_other_deg1.07737882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1765470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53724.35177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72215610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0361521
X-RAY DIFFRACTIONr_chiral_restr0.1230.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02785
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1731.6051841
X-RAY DIFFRACTIONr_mcbond_other1.1731.6031840
X-RAY DIFFRACTIONr_mcangle_it1.8842.42324
X-RAY DIFFRACTIONr_mcangle_other1.8842.4022325
X-RAY DIFFRACTIONr_scbond_it1.7851.8941951
X-RAY DIFFRACTIONr_scbond_other1.7761.8831947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6022.6852802
X-RAY DIFFRACTIONr_long_range_B_refined6.39520.4684082
X-RAY DIFFRACTIONr_long_range_B_other6.31719.9854023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.593→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 246 -
Rwork0.238 4655 -
obs--99.98 %
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)
15.3279-0.1556-1.14051.14580.37791.36650.12290.157-0.1055-0.0858-0.08390.1564-0.0775-0.0838-0.0390.01640.0221-0.01150.0436-0.00730.0363-25.02445.3389-21.8771
22.2824-1.3453-0.24254.15050.38672.9225-0.0702-0.1622-0.10540.24690.1736-0.21510.04320.193-0.10340.01760.0076-0.00860.0607-0.01170.04348.074511.6957-15.5348
33.8183-0.19061.65920.8241-0.23631.87360.0384-0.05460.03430.1326-0.05380.1183-0.0794-0.04260.01540.03430.00930.01950.0495-0.00670.0188-29.913216.1736-0.8006
41.5498-0.3356-1.81451.39770.91355.40940.0982-0.04620.0025-0.1991-0.0282-0.0439-0.37670.0325-0.070.04510.00510.00560.0097-0.00340.0068-0.214924.2666-7.398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 202
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B115 - 240

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