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- PDB-6fr4: 003 TCR Study of CDR Loop Flexibility -

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Basic information

Entry
Database: PDB / ID: 6fr4
Title003 TCR Study of CDR Loop Flexibility
Components
  • TCR 003 Beta Chain
  • TCR 003 alpha chain
KeywordsIMMUNE SYSTEM / 003 TCR / CDR Flexibility / 3D Structure / MHC Class I
Function / homology
Function and homology information


T cell receptor complex
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsRizkallah, P.J. / Cole, D.K.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Flexibility Study of CDRs in 003 TCR
Authors: Rizkallah, P.J. / 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 / 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCR 003 alpha chain
B: TCR 003 Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,23624
Polymers49,6932
Non-polymers1,54322
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint13 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.280, 81.290, 65.090
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein TCR 003 alpha chain


Mass: 22241.654 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) / References: UniProt: Q6NSA1
#2: Protein TCR 003 Beta Chain


Mass: 27451.434 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 , 4 types, 636 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: .1M Na Acetate, 0.1M CaCl2, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.28→43.28 Å / Num. obs: 109519 / % possible obs: 94.8 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.049 / Net I/σ(I): 15.5
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.423 / Num. unique obs: 5708 / CC1/2: 0.725 / Rrim(I) all: 0.543 / % possible all: 67.1

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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: 6EH4

6eh4


Resolution: 1.28→43.28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.689 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19027 5475 5 %RANDOM
Rwork0.16763 ---
obs0.16875 104016 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.13 Å2
2---0.67 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.28→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 100 614 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194006
X-RAY DIFFRACTIONr_bond_other_d0.0030.023515
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9515453
X-RAY DIFFRACTIONr_angle_other_deg1.06838238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55224.694196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05615646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1821525
X-RAY DIFFRACTIONr_chiral_restr0.1190.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214599
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02830
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_it0.6640.7041949
X-RAY DIFFRACTIONr_mcbond_other0.6440.7011947
X-RAY DIFFRACTIONr_mcangle_it1.1191.0512480
X-RAY DIFFRACTIONr_mcangle_other1.1211.0532481
X-RAY DIFFRACTIONr_scbond_it1.1420.8952057
X-RAY DIFFRACTIONr_scbond_other1.1420.8952058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5781.2472963
X-RAY DIFFRACTIONr_long_range_B_refined6.12210.7074346
X-RAY DIFFRACTIONr_long_range_B_other6.0239.5824200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.28→1.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 281 -
Rwork0.262 5421 -
obs--66.95 %
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)
11.18060.0012-0.08970.96780.1932.2204-0.04190.11950.0187-0.1269-0.0324-0.0056-0.0037-0.02370.07430.04790.0015-0.00610.09630.0030.035815.649-48.0338114.0817
22.02061.37560.27713.51220.8051.54430.0319-0.101-0.13850.07860.0042-0.11080.08120.0433-0.0360.02510.0027-0.00240.12790.02070.0289-0.2751-65.4472139.5856
31.16370.7386-0.19383.2795-0.19371.1137-0.03850.04350.05980.04210.0184-0.0146-0.01270.04990.020.068-0.0039-0.00210.0860.00170.0049-2.0843-53.2507100.9849
40.99680.27620.40871.3380.78982.5224-0.0136-0.0398-0.0584-0.12020.0018-0.0070.1159-0.00830.01180.038-0.00280.00570.08620.01240.0062-12.7362-62.186127.6936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 203
3X-RAY DIFFRACTION3B1 - 114
4X-RAY DIFFRACTION4B115 - 244

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