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- PDB-4grm: The crystal structure of the high affinity TCR A6 -

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Basic information

Entry
Database: PDB / ID: 4grm
TitleThe crystal structure of the high affinity TCR A6
Components
  • A6 alpha chain
  • A6 beta chain
KeywordsIMMUNE SYSTEM / high-affinity TCR / c134 modification / TAX peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBorbulevych, O.Y. / Scott, D.R. / Baker, B.M.
CitationJournal: Front Immunol / Year: 2013
Title: Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode.
Authors: Cole, D.K. / Sami, M. / Scott, D.R. / Rizkallah, P.J. / Borbulevych, O.Y. / Todorov, P.T. / Moysey, R.K. / Jakobsen, B.K. / Boulter, J.M. / Baker, B.M. / Li, Y.I.
History
DepositionAug 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: A6 alpha chain
B: A6 beta chain
C: A6 alpha chain
D: A6 beta chain


Theoretical massNumber of molelcules
Total (without water)97,6964
Polymers97,6964
Non-polymers00
Water1,06359
1
A: A6 alpha chain
B: A6 beta chain


Theoretical massNumber of molelcules
Total (without water)48,8482
Polymers48,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-27 kcal/mol
Surface area19680 Å2
MethodPISA
2
C: A6 alpha chain
D: A6 beta chain


Theoretical massNumber of molelcules
Total (without water)48,8482
Polymers48,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-28 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.491, 51.969, 95.218
Angle α, β, γ (deg.)90.00, 104.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.995738, -0.017842, 0.090486), (0.020784, 0.999282, -0.031679), (-0.089855, 0.033425, 0.995394)-49.74228, 0.59343, 4.49022

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Components

#1: Protein A6 alpha chain


Mass: 21395.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein A6 beta chain


Mass: 27452.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 21, 2009
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 58107 / Num. obs: 57468 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.12 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.775 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.21 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29495 2918 5.1 %RANDOM
Rwork0.23436 ---
all0.23745 58240 --
obs0.23745 54513 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.939 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→18.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6553 0 0 59 6612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9389162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5324.696313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.045151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9641533
X-RAY DIFFRACTIONr_chiral_restr0.1320.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215235
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 177 -
Rwork0.301 3768 -
obs--96.45 %

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