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- PDB-3vxt: T36-5 TCR specific for HLA-A24-Nef134-10 -

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Basic information

Entry
Database: PDB / ID: 3vxt
TitleT36-5 TCR specific for HLA-A24-Nef134-10
Components
  • T36-5 TCR alpha chain
  • T36-5 TCR beta chain
KeywordsIMMUNE SYSTEM / HIV-1 / NEF / T CELL RECEPTOR / IMMUNOGLOBURIN DOMAIN / TCR / IMMUNE RESPONSE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A.
CitationJournal: SCI REP / Year: 2013
Title: Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection
Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. ...Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. / Fukai, S. / Iwamoto, A.
History
DepositionSep 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: 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 1.4Oct 30, 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
C: T36-5 TCR alpha chain
D: T36-5 TCR beta chain
A: T36-5 TCR alpha chain
B: T36-5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)100,6854
Polymers100,6854
Non-polymers00
Water1,946108
1
C: T36-5 TCR alpha chain
D: T36-5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-25 kcal/mol
Surface area21480 Å2
MethodPISA
2
A: T36-5 TCR alpha chain
B: T36-5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-28 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.768, 65.036, 92.275
Angle α, β, γ (deg.)91.300, 94.190, 105.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein T36-5 TCR alpha chain


Mass: 22764.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Protein T36-5 TCR beta chain


Mass: 27577.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.63 Å3/Da / Density % sol: 53.18 % / Mosaicity: 0.596 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M potassium sulfate, 0.1M MES, 15% PEG8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32447 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.038 / Χ2: 1.675 / Net I/σ(I): 23.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.591.90.22228671.149181.6
2.59-2.692.10.19929681.161183.6
2.69-2.822.20.15930231.166186.5
2.82-2.962.50.11931461.378188.7
2.96-3.152.80.08932671.573192.9
3.15-3.393.30.06134401.648196.7
3.39-3.733.60.04734731.837198.5
3.73-4.273.60.03634711.904197.9
4.27-5.383.70.02834771.769198.7
5.38-503.70.02833151.983193.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.3refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KXF

3kxf


Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3220 9.1 %RANDOM
Rwork0.2304 ---
obs-32246 91.5 %-
Solvent computationBsol: 48.6118 Å2
Displacement parametersBiso max: 144.81 Å2 / Biso mean: 69.1722 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.055 Å2-10.952 Å2-1.108 Å2
2--10.097 Å2-11.829 Å2
3----12.151 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 0 108 7080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6871.5
X-RAY DIFFRACTIONc_scbond_it1.9422
X-RAY DIFFRACTIONc_mcangle_it3.0212
X-RAY DIFFRACTIONc_scangle_it3.1242.5
LS refinement shellResolution: 2.5→2.66 Å
RfactorNum. reflection% reflection
Rfree0.427 --
Rwork0.388 --
obs-456 79 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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