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- PDB-3qh3: The crystal structure of TCR A6 -

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Basic information

Entry
Database: PDB / ID: 3qh3
TitleThe crystal structure of TCR A6
Components
  • A6 alpha chain
  • A6 beta chain
KeywordsIMMUNE SYSTEM / TAX peptide / Tel1p peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism.
Authors: Scott, D.R. / Borbulevych, O.Y. / Piepenbrink, K.H. / Corcelli, S.A. / Baker, B.M.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A6 alpha chain
B: A6 beta chain
C: A6 alpha chain
D: A6 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,62719
Polymers97,5464
Non-polymers1,08115
Water4,612256
1
A: A6 alpha chain
B: A6 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,32910
Polymers48,7732
Non-polymers5578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-14 kcal/mol
Surface area21220 Å2
MethodPISA
2
C: A6 alpha chain
D: A6 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2979
Polymers48,7732
Non-polymers5257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-18 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.247, 51.735, 96.336
Angle α, β, γ (deg.)90.00, 105.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein A6 alpha chain


Mass: 21395.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Protein A6 beta chain


Mass: 27377.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 30%, TRIS 0.1M, pH 8.5, vapor diffusion, sitting drop, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2008
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.19→20 Å / Num. all: 44886 / Num. obs: 44707 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.19-2.243.50.578199.1
2.24-2.283.50.517199.3
2.28-2.323.50.491199.4
2.32-2.373.60.419198.8
2.37-2.423.50.372198.9
2.42-2.483.50.343199.8
2.48-2.543.50.272199.7
2.54-2.613.50.236199.9
2.61-2.683.50.193199.9
2.68-2.773.50.1671100
2.77-2.873.50.1441100
2.87-2.983.60.107199.5
2.98-3.123.60.087199.8
3.12-3.283.50.073199.6
3.28-3.493.50.0631100
3.49-3.763.50.0551100
3.76-4.133.40.0471100
4.13-4.723.50.037199.8
4.72-5.923.70.0351100
5.92-203.40.032199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→19.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.064 / SU ML: 0.181 / SU R Cruickshank DPI: 0.3482 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27411 2254 5 %RANDOM
Rwork0.20165 ---
obs0.20527 42439 100 %-
all-45277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.22 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.19→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 70 256 7160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9459645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4045881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92124.767344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.407151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6271539
X-RAY DIFFRACTIONr_chiral_restr0.1670.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215509
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.54385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67127098
X-RAY DIFFRACTIONr_scbond_it2.5732715
X-RAY DIFFRACTIONr_scangle_it3.8064.52541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.243 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 150 -
Rwork0.259 2703 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5250.7102-0.78072.4495-1.28653.5788-0.05450.29960.3196-0.1087-0.0685-0.195-0.27170.16910.1230.12050.00020.01950.11030.00650.103764.462949.494973.6994
25.48370.68780.72787.3691.05636.26840.10060.3508-1.0293-0.30850.03530.04751.15470.1586-0.13590.33340.0423-0.00760.1007-0.01630.280744.486224.775283.0854
34.25321.6362-0.85496.5807-0.92663.5359-0.07060.26370.2767-0.01920.15170.0349-0.2262-0.1559-0.08110.16190.00590.02350.23140.01250.073651.289751.423754.5516
42.463-0.0403-0.48311.59740.88086.4415-0.05530.3349-0.3298-0.13420.13540.03580.3649-0.1568-0.08010.1055-0.0375-0.00940.09170.00910.181134.949933.47372.6536
55.64930.62061.02213.3325-2.26247.8926-0.23940.63360.74280.0258-0.1594-0.3434-0.60860.43040.39880.135-0.0085-0.06140.28370.13290.2935109.154748.503771.3941
66.69911.74941.66897.55551.52986.91810.08390.3247-0.6818-0.09120.1139-0.46080.82980.3864-0.19790.27050.0498-0.00440.11220.02890.128589.385224.714584.0643
73.69581.74270.05746.2351-1.1553.4724-0.17520.21820.28650.0219-0.0035-0.134-0.15980.14440.17870.07840.0444-0.00010.20880.040.049393.370949.901253.9969
81.5231-0.05190.61221.80790.43335.54130.01020.0826-0.1736-0.02460.0336-0.00720.14360.0274-0.04380.0367-0.00850.01550.0088-0.00770.052279.16833.158574.4463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION2A116 - 194
3X-RAY DIFFRACTION3B1 - 115
4X-RAY DIFFRACTION4B116 - 245
5X-RAY DIFFRACTION5C1 - 115
6X-RAY DIFFRACTION6C116 - 194
7X-RAY DIFFRACTION7D1 - 115
8X-RAY DIFFRACTION8D116 - 245

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