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- PDB-5z11: Crystal Structure of Grass Carp CD8 alpha alpha Homodimers -

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Basic information

Entry
Database: PDB / ID: 5z11
TitleCrystal Structure of Grass Carp CD8 alpha alpha Homodimers
ComponentsCD8 alpha chain
KeywordsIMMUNE SYSTEM / Grass carp / CD8 alpha / crystal structure / MHC / evolution.
Function / homology
Function and homology information


adaptive immune response / plasma membrane
Similarity search - Function
CD8 alpha subunit / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesCtenopharyngodon idella (grass carp)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.35 Å
AuthorsWang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNO.31230074 China
CitationJournal: To Be Published
Title: Crystal Structure of the Grass Carp CD8 alpha alpha Homodimers Indicates a Dramatic Evolution of CD8 from Ectotherms to Endotherms.
Authors: Wang, J. / Zhang, L.
History
DepositionDec 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Assembly

Deposited unit
A: CD8 alpha chain
B: CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)28,3282
Polymers28,3282
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.910, 47.910, 242.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CD8 alpha chain


Mass: 14164.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Production host: Escherichia coli (E. coli) / References: UniProt: C7FF18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.987 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 12041 / % possible obs: 99.8 % / Redundancy: 12.4 % / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.48 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.422 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25804 612 4.8 %RANDOM
Rwork0.20027 ---
obs0.20308 12041 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.679 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.35→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 0 38 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021641
X-RAY DIFFRACTIONr_bond_other_d0.0020.021519
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9462205
X-RAY DIFFRACTIONr_angle_other_deg0.9813.0033537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3525206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83425.26376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.286156
X-RAY DIFFRACTIONr_chiral_restr0.110.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
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_it4.4364.768818
X-RAY DIFFRACTIONr_mcbond_other4.4334.763817
X-RAY DIFFRACTIONr_mcangle_it6.1857.1271020
X-RAY DIFFRACTIONr_mcangle_other6.1837.1331021
X-RAY DIFFRACTIONr_scbond_it6.25.469823
X-RAY DIFFRACTIONr_scbond_other6.1995.46821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3277.8261183
X-RAY DIFFRACTIONr_long_range_B_refined11.20753.7051703
X-RAY DIFFRACTIONr_long_range_B_other11.21453.7161700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 48 -
Rwork0.261 882 -
obs--99.89 %

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