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- PDB-5eb9: Crystal Structure Of Chicken CD8aa Homodimer -

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Basic information

Entry
Database: PDB / ID: 5eb9
TitleCrystal Structure Of Chicken CD8aa Homodimer
ComponentsCD8 alpha chain
KeywordsIMMUNE SYSTEM / CD8 / Co-receptor / Immunology
Function / homology
Function and homology information


cytotoxic T cell differentiation / T cell mediated immunity / cell surface receptor signaling pathway / external side of plasma membrane
Similarity search - Function
CD8 alpha subunit / 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 / Immunoglobulins ...CD8 alpha subunit / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.006 Å
AuthorsLiu, Y.J. / Qi, J.X. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
973 Project2013CB835302 China
CitationJournal: Sci Rep / Year: 2016
Title: The structural basis of chicken, swine and bovine CD8 alpha alpha dimers provides insight into the co-evolution with MHC I in endotherm species.
Authors: Liu, Y. / Li, X. / Qi, J. / Zhang, N. / Xia, C.
History
DepositionOct 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)13,6601
Polymers13,6601
Non-polymers00
Water1,56787
1
A: CD8 alpha chain

A: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)27,3212
Polymers27,3212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1660 Å2
ΔGint-15 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.360, 87.063, 70.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CD8 alpha chain


Mass: 13660.378 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QR64
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium formate, 20% w/v Polyethylene glycol 3350
PH range: 7.0-7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 11, 2012
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9518 / % possible obs: 97.5 % / Redundancy: 5 % / Net I/σ(I): 20.624
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.824 / % possible all: 78.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.52refinement
RefinementResolution: 2.006→23.09 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 0.12 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 436 4.78 %
Rwork0.2367 --
obs0.238 9124 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.245 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5802 Å2-0 Å20 Å2
2---10.416 Å2-0 Å2
3---12.9962 Å2
Refinement stepCycle: LAST / Resolution: 2.006→23.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 0 87 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016947
X-RAY DIFFRACTIONf_angle_d1.3641273
X-RAY DIFFRACTIONf_dihedral_angle_d21.254355
X-RAY DIFFRACTIONf_chiral_restr0.131127
X-RAY DIFFRACTIONf_plane_restr0.006171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0058-2.29580.30341300.26522629X-RAY DIFFRACTION87
2.2958-2.89160.29991420.24452956X-RAY DIFFRACTION97
2.8916-23.09150.23971640.22413103X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.1859 Å / Origin y: 11.3681 Å / Origin z: 3.5294 Å
111213212223313233
T0.2314 Å2-0.0058 Å2-0.0138 Å2-0.2204 Å2-0.0123 Å2--0.222 Å2
L0.1937 °2-0.1356 °2-0.1061 °2-0.3569 °2-0.0231 °2--0.2493 °2
S0.036 Å °-0.0504 Å °-0.0563 Å °0.1122 Å °-0.0518 Å °0.0716 Å °-0.1218 Å °0.0185 Å °0.0136 Å °
Refinement TLS groupSelection details: all

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