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- PDB-1tvd: VARIABLE DOMAIN OF T CELL RECEPTOR DELTA CHAIN -

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Basic information

Entry
Database: PDB / ID: 1tvd
TitleVARIABLE DOMAIN OF T CELL RECEPTOR DELTA CHAIN
ComponentsT CELL RECEPTOR
KeywordsIMMUNORECEPTOR / TCR / DELTA CHAIN / VARIABLE DOMAIN
Function / homology
Function and homology information


T cell receptor complex / immunoglobulin complex / adaptive immune response / immune response / innate immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / T cell receptor delta variable 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsLi, H.M. / Lebedeva, M.I. / Llera, A.S. / Fields, B.A. / Brenner, M.B. / Mariuzza, R.A.
Citation
Journal: Nature / Year: 1998
Title: Structure of the Vdelta domain of a human gammadelta T-cell antigen receptor.
Authors: Li, H. / Lebedeva, M.I. / Llera, A.S. / Fields, B.A. / Brenner, M.B. / Mariuzza, R.A.
#1: Journal: Protein Sci. / Year: 1996
Title: Cloning, Expression, and Crystallization of the V Delta Domain of a Human Gamma Delta T-Cell Receptor
Authors: Lebedeva, M.I. / Fields, B.A. / Spits, H. / Panchamoorthy, G. / Brenner, M.B. / Mariuzza, R.A.
History
DepositionOct 19, 1997Processing site: BNL
Revision 1.0Apr 22, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T CELL RECEPTOR
B: T CELL RECEPTOR


Theoretical massNumber of molelcules
Total (without water)26,2912
Polymers26,2912
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-8 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.940, 49.080, 61.670
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: (-0.971829, -0.032294, -0.233465), (-0.116371, -0.795655, 0.594466), (-0.204956, 0.604888, 0.769483)
Vector: 25.5156, -15.165, 8.277)

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Components

#1: Protein T CELL RECEPTOR / ES204 V DELTA


Mass: 13145.624 Da / Num. of mol.: 2 / Fragment: DELTA CHAIN, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: ES204 / Plasmid: PET26B(+) / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 BL21 (DE3) / References: PIR: S04934, UniProt: A0JD37*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5
Details: 0.65-0.75M SODIUM CITRATE 0.1M SODIUM CACODYLATE, PH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Lebedeva, M.I., (1996) Protein Sci., 5, 2638. / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.9 Msodium citrate1reservoir
30.1 Msodium cacodylate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: SIEMENS / Detector: CCD / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 44342 / % possible obs: 83.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3 / Rsym value: 0.166 / % possible all: 53.7
Reflection
*PLUS
Num. obs: 13905 / Num. measured all: 44342

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Processing

Software
NameVersionClassification
MADNESdata collection
XSCALEdata scaling
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1322 10 %RANDOM
Rwork0.161 ---
obs0.161 13810 83.3 %-
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 0 309 2203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
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: 1.9→1.99 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.284 110 10 %
Rwork0.224 810 -
obs--53.1 %
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
Rfactor all: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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