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- PDB-8irq: Larimichthys crocea IFNd -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8irq
TitleLarimichthys crocea IFNd
ComponentsInterferon d
KeywordsCYTOKINE / interferon / antiviral
Function / homology
Function and homology information


cytokine receptor binding / response to exogenous dsRNA / cytokine activity / defense response to virus / extracellular space
Similarity search - Function
Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Four-helical cytokine-like, core / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesLarimichthys crocea (large yellow croaker)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChen, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Immunol. / Year: 2024
Title: Structural and Functional Characterization of a Fish Type I Subgroup d IFN Reveals Its Binding to Receptors.
Authors: Guan, Y. / Chen, J. / Guan, H. / Chen, T.T. / Teng, Y. / Wei, Z. / Li, Z. / Ouyang, S. / Chen, X.
History
DepositionMar 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Oct 1, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon d


Theoretical massNumber of molelcules
Total (without water)18,8991
Polymers18,8991
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.378, 38.813, 51.091
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon d


Mass: 18898.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Larimichthys crocea (large yellow croaker)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4AIP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion / Details: PEG 2000ME, Trisbase/Hydrochloric acid

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→47.09 Å / Num. obs: 22157 / % possible obs: 95.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 27.52
Reflection shellResolution: 1.49→1.543 Å / CC1/2: 0.999

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXv1.0refinement
HKL-2000data scaling
SHELXTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→47.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.979 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1107 4.8 %RANDOM
Rwork0.16214 ---
obs0.16447 22157 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.859 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20.02 Å2
2---1.94 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.49→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 0 151 1345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131230
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171101
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.6241659
X-RAY DIFFRACTIONr_angle_other_deg1.5891.582561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84623.04369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.115220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.737157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
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_it3.0682.26607
X-RAY DIFFRACTIONr_mcbond_other3.0582.258606
X-RAY DIFFRACTIONr_mcangle_it3.3913.39757
X-RAY DIFFRACTIONr_mcangle_other3.3923.393758
X-RAY DIFFRACTIONr_scbond_it4.452.743623
X-RAY DIFFRACTIONr_scbond_other4.4482.745624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.773.915903
X-RAY DIFFRACTIONr_long_range_B_refined4.94329.5811529
X-RAY DIFFRACTIONr_long_range_B_other4.74529.0081499
X-RAY DIFFRACTIONr_rigid_bond_restr3.77332331
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.524 Å
RfactorNum. reflection% reflection
Rfree0.269 108 -
Rwork0.229 1639 -
obs--98.59 %

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