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- PDB-1ac6: CRYSTAL STRUCTURE OF A VARIABLE DOMAIN MUTANT OF A T-CELL RECEPTO... -

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Basic information

Entry
Database: PDB / ID: 1ac6
TitleCRYSTAL STRUCTURE OF A VARIABLE DOMAIN MUTANT OF A T-CELL RECEPTOR ALPHA CHAIN
ComponentsT-CELL RECEPTOR ALPHA
KeywordsRECEPTOR / V ALPHA DOMAIN / SITE-DIRECTED MUTAGENESIS / THREE-DIMENSIONAL STRUCTURE / GLYCOPROTEIN
Function / homology
Function and homology information


T cell receptor complex / adaptive immune response
Similarity search - Function
: / 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 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
T-cell receptor alpha chain V region CTL-F3 / TRAV6D-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, H.-M. / Mariuzza, R.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Dual conformations of a T cell receptor V alpha homodimer: implications for variability in V alpha V beta domain association.
Authors: Li, H. / Lebedeva, M.I. / Ward, E.S. / Mariuzza, R.A.
#1: Journal: Nature / Year: 1996
Title: Crystal Structure of a T-Cell Receptor Beta-Chain Complexed with a Superantigen
Authors: Fields, B.A. / Malchiodi, E.L. / Li, H. / Ysern, X. / Stauffacher, C.V. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A.
#2: Journal: Science / Year: 1995
Title: Crystal Structure of the Beta Chain of a T Cell Antigen Receptor
Authors: Bentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A.
#3: Journal: Science / Year: 1995
Title: Crystal Structure of the V Alpha Domain of a T Cell Antigen Receptor
Authors: Fields, B.A. / Ober, B. / Malchiodi, E.L. / Lebedeva, M.I. / Braden, B.C. / Ysern, X. / Kim, J.K. / Shao, X. / Ward, E.S. / Mariuzza, R.A.
History
DepositionFeb 13, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 20, 2013Group: Database references
Revision 1.4Apr 3, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 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: T-CELL RECEPTOR ALPHA
B: T-CELL RECEPTOR ALPHA


Theoretical massNumber of molelcules
Total (without water)24,2092
Polymers24,2092
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.430, 64.820, 45.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.86457, -0.497718, 0.069259), (-0.501079, 0.843467, -0.193609), (0.037945, -0.202092, -0.978631)
Vector: 64.7856, 19.1277, 16.1694)

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Components

#1: Protein T-CELL RECEPTOR ALPHA


Mass: 12104.274 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN / Mutation: yes / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P06323, UniProt: Q5R1F5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.7
Details: PROTEIN WAS CRYSTALLIZED FROM 5.0M SODIUM FORMATE, PH 7.7 IN HANGING DROPS AT ROOM TEMPERATURE., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
22.50 Msodium formate1drop
35.0 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→26.41 Å / Num. obs: 9957 / % possible obs: 78.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.38 / Rsym value: 0.406 / % possible all: 73
Reflection
*PLUS
Num. measured all: 26767
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
XENGEN21data collection
XENGEN21data reduction
AMoREphasing
X-PLOR3.1refinement
XENGENV. 2.1data reduction
XENGENV. 2.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VALPHA WILDTYPE HOMODIMER STRUCTURE OF 1934.4 TCR

Resolution: 2.3→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 560 7.8 %RANDOM
Rwork0.161 ---
obs0.161 7161 73.7 %-
Displacement parametersBiso mean: 24.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 0 116 1826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.286 37 5.9 %
Rwork0.226 287 -
obs--51.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 7850 / Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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