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- PDB-2axh: Crystal structures of T cell receptor beta chains related to rheu... -

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Entry
Database: PDB / ID: 2axh
TitleCrystal structures of T cell receptor beta chains related to rheumatoid arthritis
ComponentsT cell receptor beta chain
KeywordsIMMUNE SYSTEM / TCR
Function / homology
Function and homology information


PD-1 signaling / Generation of second messenger molecules / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / positive regulation of B cell activation ...PD-1 signaling / Generation of second messenger molecules / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / positive regulation of B cell activation / phagocytosis, engulfment / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / regulation of immune response / T cell receptor signaling pathway / immune response / external side of plasma membrane / defense response to bacterium / innate immune response / membrane / integral component of membrane / plasma membrane
Immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin C1-set / Immunoglobulin-like domain superfamily / Immunoglobulin C1-set domain / Immunoglobulin-like fold
T cell receptor beta constant 1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLi, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
Authors: Li, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 5, 2005 / Release: Sep 20, 2005
RevisionDateData content typeGroupProviderType
1.0Sep 20, 2005Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T cell receptor beta chain
B: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)55,2152
Polymers55,2152
Non-polymers00
Water1,62190
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-7 kcal/mol
Surface area23280 Å2
MethodPISA
2
A: T cell receptor beta chain
B: T cell receptor beta chain
x 6


Theoretical massNumber of molelcules
Total (without water)331,28712
Polymers331,28712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area41980 Å2
ΔGint-138 kcal/mol
Surface area117140 Å2
MethodPISA
3
A: T cell receptor beta chain
B: T cell receptor beta chain

A: T cell receptor beta chain
B: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)110,4294
Polymers110,4294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
Buried area10740 Å2
ΔGint-33 kcal/mol
Surface area42300 Å2
MethodPISA
4
A: T cell receptor beta chain

A: T cell receptor beta chain

B: T cell receptor beta chain

B: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)110,4294
Polymers110,4294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/21
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
Buried area7150 Å2
ΔGint-33 kcal/mol
Surface area45890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)187.334, 187.334, 86.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

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Components

#1: Protein/peptide T cell receptor beta chain


Mass: 27607.275 Da / Num. of mol.: 2 / Fragment: extracellular domain / Mutation: F104Y, C187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01850
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.95 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6-0.7m sodium citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source

Beamline: X25 / Site: NSLS / Source: SYNCHROTRON

Diffraction-IDWavelength (Å)
10.9794
20.9798
30.93
Detector
TypeDiffraction-IDDetectorDate
ADSC QUANTUM 41CCDJun 8, 2003
2
3
Radiation

Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength-ID: 1

Diffraction-IDMonochromatorProtocol
1Si 111MAD
2
3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97981
30.931
ReflectionResolution: 2.7→39.2 Å / Num. all: 24987 / Num. obs: 24387 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 79.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 35
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.478 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→39.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2028564.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1802 7.4 %RANDOM
Rwork0.237 ---
Obs0.237 24387 97.6 %-
All-24987 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2572 Å2 / ksol: 0.359192 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å24.44 Å20 Å2
2---2.95 Å20 Å2
3---5.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 0 90 3974
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 302 7.4 %
Rwork0.317 3768 -
Obs--99.5 %
Xplor file

Refinement-ID: X-RAY DIFFRACTION

Serial noParam fileTopol file
1protein_rep.paramprotein.top
2water_rep.paramwater_rep.top

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