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- PDB-2q3a: Crystal Structure of Rhesus Macaque CD8 Alpha-Alpha Homodimer -

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Basic information

Entry
Database: PDB / ID: 2q3a
TitleCrystal Structure of Rhesus Macaque CD8 Alpha-Alpha Homodimer
ComponentsCD8
KeywordsIMMUNE SYSTEM / rhesus macaque / CD8 homodimer / immunoglobulin / MHC / complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPeng, H. / Chen, Y. / Zong, L. / Gao, F. / Liu, Y. / Gao, G.F.
CitationJournal: To be Published
Title: Crystal Structure of Rhesus Macaque CD8 Homodimer Sheds the Lights on the Molecular Basis of Rhesus Macaque MHC class I with CD8 Complex
Authors: Zong, L. / Chen, Y. / Peng, H. / Cole, D.K. / Gao, F. / Liu, Y. / Gao, G.F.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN the UNP DATABASE AT THE TIME OF ...sequence THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE IN the UNP DATABASE AT THE TIME OF PROCESSING. Author stated THE SEQUENCE OF THIS PROTEIN IS UNDER GeneBank ACCESSION CODE: XP_001092778

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD8
B: CD8


Theoretical massNumber of molelcules
Total (without water)27,1732
Polymers27,1732
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.543, 56.259, 82.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CD8


Mass: 13586.456 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Details: Indian origin / Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 24

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M potassium phosphate monobasic, 20% w/v Polyethylene glycol 8,000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 5, 2007
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 11471 / Num. obs: 11313 / Redundancy: 6.6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.136
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1588

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKJ

1akj


Resolution: 2.2→35.85 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2566 719 RANDOM
Rwork0.2133 --
all-7021 -
obs-7018 -
Displacement parametersBiso mean: 20.296 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 133 1984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006192
X-RAY DIFFRACTIONc_angle_deg1.33493

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