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- PDB-7x45: Grass carp interferon gamma related -

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Basic information

Entry
Database: PDB / ID: 7x45
TitleGrass carp interferon gamma related
ComponentsInterferon gamma
KeywordsCYTOKINE / interferon gamma / interferon gamma related / fish / grass carp
Function / homologyInterferon gamma / type II interferon receptor binding / Four-helical cytokine-like, core / immune response / extracellular region / Interferon gamma
Function and homology information
Biological speciesCtenopharyngodon idella (grass carp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsWang, J. / Zou, J. / Zhu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030112 China
CitationJournal: J Immunol. / Year: 2022
Title: Novel Dimeric Architecture of an IFN-gamma-Related Cytokine Provides Insights into Subfunctionalization of Type II IFNs in Teleost Fish.
Authors: Zhu, X. / Wang, J. / Jia, Z. / Feng, J. / Wang, B. / Wang, Z. / Liu, Q. / Wu, K. / Huang, W. / Zhao, X. / Dang, H. / Zou, J.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon gamma
B: Interferon gamma


Theoretical massNumber of molelcules
Total (without water)39,2952
Polymers39,2952
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-61 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.580, 48.580, 208.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Interferon gamma


Mass: 19647.725 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: C0LEE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 1.81 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) PEG 400, 100 mM sodium cacodylate/Hydrochloric acid PH 6.5, 200 mM Lithium sulfat

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 2.26→42.07 Å / Num. obs: 18555 / % possible obs: 99.8 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.4
Reflection shellResolution: 2.26→2.33 Å / Rmerge(I) obs: 1.146 / Num. unique obs: 16390

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→42.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.1588 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.202 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2683 691 5.059 %
Rwork0.2208 12969 -
all0.223 --
obs-13660 99.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.082 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20.022 Å20 Å2
2--0.044 Å2-0 Å2
3----0.143 Å2
Refinement stepCycle: LAST / Resolution: 2.26→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 0 36 2042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.3190.22540.2951X-RAY DIFFRACTION99.8014
2.319-2.3820.255430.238914X-RAY DIFFRACTION100
2.382-2.4510.303530.239897X-RAY DIFFRACTION100
2.451-2.5270.339530.234869X-RAY DIFFRACTION100
2.527-2.6090.299480.241828X-RAY DIFFRACTION100
2.609-2.7010.374520.242837X-RAY DIFFRACTION100
2.701-2.8030.25260.226781X-RAY DIFFRACTION100
2.803-2.9170.343390.254772X-RAY DIFFRACTION100
2.917-3.0460.374170.244757X-RAY DIFFRACTION100
3.046-3.1950.314280.259696X-RAY DIFFRACTION100
3.195-3.3670.175290.1675X-RAY DIFFRACTION100
3.367-3.5710.341410.224631X-RAY DIFFRACTION100
3.571-3.8170.325240.228605X-RAY DIFFRACTION100
3.817-4.1210.262370.218558X-RAY DIFFRACTION100
4.121-4.5130.163300.1503X-RAY DIFFRACTION100
4.513-5.0430.246360.181468X-RAY DIFFRACTION100
5.043-5.8180.234260.231415X-RAY DIFFRACTION100
5.818-7.1130.311290.258354X-RAY DIFFRACTION100
7.1-100.25270.193174X-RAY DIFFRACTION99.4505
7.113-100.257190.147284X-RAY DIFFRACTION100

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