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- PDB-7d9m: grass carp interleukin-2 -

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Basic information

Entry
Database: PDB / ID: 7d9m
Titlegrass carp interleukin-2
ComponentsInterleukin
KeywordsCYTOKINE / interleukin-2 / fish / grass carp
Function / homologyregulation of macromolecule metabolic process / Interleukin-15/Interleukin-21 family / Interleukin 15 / cytokine receptor binding / Four-helical cytokine-like, core / cytokine activity / immune response / extracellular space / Interleukin
Function and homology information
Biological speciesCtenopharyngodon idella (grass carp)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.66 Å
AuthorsJunya, w. / Jun, z.
CitationJournal: Dev.Comp.Immunol. / Year: 2020
Title: Structural insights into the co-evolution of IL-2 and its private receptor in fish.
Authors: Wang, J. / Wang, W. / Xu, J. / Jia, Z. / Liu, Q. / Zhu, X. / Xia, C. / Zou, J.
History
DepositionOct 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Interleukin
D: Interleukin


Theoretical massNumber of molelcules
Total (without water)27,9762
Polymers27,9762
Non-polymers00
Water0
1
B: Interleukin

D: Interleukin


Theoretical massNumber of molelcules
Total (without water)27,9762
Polymers27,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.090, 83.090, 302.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Interleukin /


Mass: 13987.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: IL-2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6NYT7

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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: 5.4 Å3/Da / Density % sol: 77.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.4 M Sodium phosphate monobasic monohydrate, Potassium Phosphate dibasic (pH 8.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.66→45 Å / Num. obs: 17766 / % possible obs: 93.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.62 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.3
Reflection shellResolution: 2.66→10 Å / Num. unique obs: 8666 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.66→38.42 Å / SU ML: 0.4724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.5505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.4117 860 4.84 %
Rwork0.3773 16906 -
obs0.3779 17766 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.86 Å2
Refinement stepCycle: LAST / Resolution: 2.66→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 0 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021878
X-RAY DIFFRACTIONf_angle_d1.17462526
X-RAY DIFFRACTIONf_chiral_restr0.0475284
X-RAY DIFFRACTIONf_plane_restr0.0066324
X-RAY DIFFRACTIONf_dihedral_angle_d20.754246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.820.3651900.34611930X-RAY DIFFRACTION66.49
2.82-3.040.39531470.35922893X-RAY DIFFRACTION99.74
3.04-3.350.39721440.37432934X-RAY DIFFRACTION100
3.35-3.830.41811430.35582943X-RAY DIFFRACTION99.68
3.83-4.830.41151600.35283005X-RAY DIFFRACTION99.91
4.83-38.420.42821760.42773201X-RAY DIFFRACTION99.53

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