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- PDB-3qjh: The crystal structure of the 5c.c7 TCR -

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Basic information

Entry
Database: PDB / ID: 3qjh
TitleThe crystal structure of the 5c.c7 TCR
Components
  • 5c.c7 alpha chain
  • 5c.c7 beta chain
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / T cell receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsEly, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).
Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 27, 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: 5c.c7 alpha chain
B: 5c.c7 beta chain
C: 5c.c7 alpha chain
D: 5c.c7 beta chain


Theoretical massNumber of molelcules
Total (without water)100,7584
Polymers100,7584
Non-polymers00
Water6,990388
1
A: 5c.c7 alpha chain
B: 5c.c7 beta chain


Theoretical massNumber of molelcules
Total (without water)50,3792
Polymers50,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area20670 Å2
MethodPISA
2
C: 5c.c7 alpha chain
D: 5c.c7 beta chain


Theoretical massNumber of molelcules
Total (without water)50,3792
Polymers50,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-24 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.166, 139.458, 61.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 5c.c7 alpha chain


Mass: 22765.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein 5c.c7 beta chain


Mass: 27613.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.7
Details: 20 % PEG3350, 0.1 M calcium chloride and Tris, pH 7.7, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→96.31 Å / Num. all: 91312 / Num. obs: 91312 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.70.2672.848922130810.26798.9
2-2.123.70.1694.546524124370.16999.4
2.12-2.273.70.1166.443953117260.11699.5
2.27-2.453.70.0858.641006109600.08599.6
2.45-2.693.70.06211.437828101180.06299.8
2.69-33.70.04215.53441792130.042100
3-3.473.70.03815.13042881930.038100
3.47-4.253.70.03118.32578369610.031100
4.25-6.013.70.02620.71999054690.026100
6.01-69.6733.40.02323.91087731540.02399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.323 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8153 / SU ML: 0.26 / σ(F): 1.07 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 8745 5 %
Rwork0.2247 --
obs0.2263 91243 99.49 %
all-91243 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.874 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 76.36 Å2 / Biso mean: 32.1987 Å2 / Biso min: 14.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.3242 Å2-0 Å20 Å2
2---3.1731 Å20 Å2
3---2.8489 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6835 0 0 388 7223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087001
X-RAY DIFFRACTIONf_angle_d1.0089489
X-RAY DIFFRACTIONf_chiral_restr0.0751036
X-RAY DIFFRACTIONf_plane_restr0.0051256
X-RAY DIFFRACTIONf_dihedral_angle_d14.3232516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.30898450.2612165271737299
1.9679-2.04670.38050.2374166231742899
2.0467-2.13980.26339000.2263164821738299
2.1398-2.25270.27818840.23651656617450100
2.2527-2.39380.298490.2463165981744799
2.3938-2.57860.28129470.25131665717604100
2.5786-2.83810.29378400.25221665117491100
2.8381-3.24860.26358810.23641669717578100
3.2486-4.09260.24618860.2111667517561100
4.0926-46.33650.21599080.19781663817546100

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