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- PDB-6fr3: 003 TCR Study of CDR Loop Flexibility -

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Basic information

Entry
Database: PDB / ID: 6fr3
Title003 TCR Study of CDR Loop Flexibility
Components
  • 003 TCR Alpha Chain
  • 003 TCR Beta Chain
KeywordsIMMUNE SYSTEM / 003 TCR / CDR Flexibility / 3D Structure / MHC Class I
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: 1.35 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 003 TCR Alpha Chain
B: 003 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,32643
Polymers49,6932
Non-polymers2,63341
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint101 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.060, 81.380, 64.790
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 003 TCR 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)
#2: Protein 003 TCR 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)
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Pact Premier solution A04: 0.1 M SPG Buffer, pH 7.0, 25% PEG w/v 1500

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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 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.35→50.69 Å / Num. obs: 95658 / % possible obs: 97.8 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.056 / Net I/σ(I): 13.9
Reflection shellResolution: 1.35→1.385 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.496 / Num. unique obs: 6641 / CC1/2: 0.752 / Rrim(I) all: 0.587 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH4

6eh4


Resolution: 1.35→50.69 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.915 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19744 4793 5 %RANDOM
Rwork0.16498 ---
obs0.16662 90837 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.18 Å2
2--0.3 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.35→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 170 486 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023912
X-RAY DIFFRACTIONr_bond_other_d0.0020.023676
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.965276
X-RAY DIFFRACTIONr_angle_other_deg1.0463.0018486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80524.574188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2321524
X-RAY DIFFRACTIONr_chiral_restr0.1360.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02930
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_it1.2370.9881846
X-RAY DIFFRACTIONr_mcbond_other1.2210.9851845
X-RAY DIFFRACTIONr_mcangle_it1.9231.4792319
X-RAY DIFFRACTIONr_mcangle_other1.931.4822320
X-RAY DIFFRACTIONr_scbond_it2.3261.3432066
X-RAY DIFFRACTIONr_scbond_other2.3271.3432066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0311.8272928
X-RAY DIFFRACTIONr_long_range_B_refined7.56410.4934653
X-RAY DIFFRACTIONr_long_range_B_other7.56410.5034654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 334 -
Rwork0.257 6304 -
obs--92.5 %
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)
11.32380.1328-0.14671.0691-0.57252.0485-0.0534-0.09070.03650.1136-0.049-0.0280.01460.02510.10240.0239-0.0041-0.00920.0261-0.00380.0611-16.3053-7.593816.0129
22.0513-1.43370.38253.55-0.58221.59080.04540.1932-0.1138-0.13350.05540.20550.0596-0.1203-0.10080.0081-0.0054-0.00190.0958-0.00540.0454-0.4308-25.058-9.3841
31.4639-0.7295-0.06842.78950.29641.5937-0.0588-0.13510.1287-0.04580.02390.0583-0.0059-0.14060.03490.04180.0027-0.01150.0485-0.01250.02511.2629-12.834729.1285
41.2823-0.32240.61311.395-0.83913.6733-0.01410.1151-0.07120.18810.03410.01830.1394-0.0346-0.020.04680.00110.00530.0175-0.01190.013111.887-21.79172.7291
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 - 242

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