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- PDB-1i9e: TCR DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1i9e
TitleTCR DOMAIN
ComponentsCYTOTOXIC TCELL VALPHA DOMAIN
KeywordsIMMUNE SYSTEM / Ig-like domain / T Cell receptor
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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell receptor alpha chain V region PHDS58
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRudolph, M.G. / Huang, M. / Teyton, L. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of an isolated V(alpha) domain of the 2C T-cell receptor.
Authors: Rudolph, M.G. / Huang, M. / Teyton, L. / Wilson, I.A.
History
DepositionMar 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: CYTOTOXIC TCELL VALPHA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9962
Polymers12,7741
Non-polymers2211
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.032, 104.032, 63.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CYTOTOXIC TCELL VALPHA DOMAIN / 2C TCR VALPHA DOMAIN


Mass: 12774.330 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF ALPHA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SC2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01738
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: di-sodium tartrate, NaCl, imidazole/HCl, pH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.100 mMprotein1drop
21 MNa2-tartrate1reservoir
30.2 M1reservoirNaCl
40.1 Mimidazole-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.783 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.783 Å / Relative weight: 1
ReflectionResolution: 2.5→37.5 Å / Num. obs: 6370 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 10.2 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 22.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 3.4 / Num. unique all: 306 / % possible all: 100
Reflection
*PLUS
Num. obs: 6260
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 100 % / Num. unique obs: 306

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Valpha domain of 2C TCR (PDB entry 1tcr) residues 1-115

1tcr


Resolution: 2.5→37.5 Å / SU B: 12.635 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.262 / ESU R Free: 0.262 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS ADDED IN THE RIDING POSITIONS DURING REFINEMENT AND HAVE NOT BEEN OUTPUT AS COORDINATES.
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 642 10.8 %RANDOM
Rwork0.20305 ---
obs0.20632 5298 95.51 %-
all-6260 --
Displacement parametersBiso mean: 25.866 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--1.36 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 14 44 963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it0.680.608
X-RAY DIFFRACTIONp_mcangle_it1.1771.177
X-RAY DIFFRACTIONp_angle_d1.5552.144
X-RAY DIFFRACTIONp_bond_d0.0143.694
LS refinement shellHighest resolution: 2.5 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.2
Refinement TLS params.Method: refined / Origin x: 97.465 Å / Origin y: 68.107 Å / Origin z: 31.935 Å
111213212223313233
T0.0929 Å20.0129 Å20.0384 Å2-0.006 Å2-0.0191 Å2--0.1598 Å2
L2.903 °2-0.9715 °21.4798 °2-3.9899 °2-2.961 °2--5.0222 °2
S0.0243 Å °0.265 Å °-0.0941 Å °-0.3343 Å °0.0912 Å °-0.0094 Å °0.0506 Å °0.0123 Å °-0.1155 Å °
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.8 % / Rfactor all: 0.20632 / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.62.144
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg21.1
X-RAY DIFFRACTIONp_mcbond_it0.68
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.57 Å / Rfactor Rfree: 0.339 / Rfactor obs: 0.242

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