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- PDB-6f1e: Crystal structure of olive flounder [Paralichthys olivaceus] inte... -

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Basic information

Entry
Database: PDB / ID: 6f1e
TitleCrystal structure of olive flounder [Paralichthys olivaceus] interferon gamma at 2.3 Angstrom resolution
ComponentsInterferon gamma
KeywordsIMMUNE SYSTEM / Interferon gamma / Four-helix bundle / Antiviral defense
Function / homology
Function and homology information


type II interferon receptor binding / cytokine activity / immune response / protein homodimerization activity / extracellular space
Similarity search - Function
Interferon gamma / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesParalichthys olivaceus (Japanese flounder)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.296 Å
AuthorsKolenko, P. / Kolarova, L. / Zahradnik, J. / Schneider, B.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic16-20507S Czech Republic
ERDFCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
Czech Academy of SciencesRVO 86652036 Czech Republic
Grant Agency of the Czech Technical University in PragueSGS16/246/OHK4/3T/14 Czech Republic
CitationJournal: Fish Shellfish Immunol. / Year: 2018
Title: Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function.
Authors: Zahradnik, J. / Kolarova, L. / Parizkova, H. / Kolenko, P. / Schneider, B.
History
DepositionNov 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Interferon gamma
B: Interferon gamma


Theoretical massNumber of molelcules
Total (without water)40,8632
Polymers40,8632
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homodimer with 40 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-79 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.238, 79.721, 94.600
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 Interferon gamma


Mass: 20431.641 Da / Num. of mol.: 2 / Mutation: Cdelta11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paralichthys olivaceus (Japanese flounder)
Gene: Ifng / Plasmid: pET26bPoli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B3IXK1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein buffer: 100 mM citrate buffer, pH 6.0 Reservoir: 3 M NaCl 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.296→49.6 Å / Num. obs: 20255 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.59-47.39.90.03748.14500.9990.0160.0498.5
2.296-2.3811.92.7110.920320.5591.1632.95697.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.296→49.59 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 9.291 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29666 978 4.8 %Random selection
Rwork0.22647 ---
obs0.22898 20204 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.012 Å2
Baniso -1Baniso -2Baniso -3
1-6.02 Å20 Å20 Å2
2---1.9 Å20 Å2
3----4.12 Å2
Refinement stepCycle: 1 / Resolution: 2.296→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 0 38 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192283
X-RAY DIFFRACTIONr_bond_other_d0.0020.022183
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9673052
X-RAY DIFFRACTIONr_angle_other_deg0.97235081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21924.444117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24215474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9811519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022447
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
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_it5.6947.2791075
X-RAY DIFFRACTIONr_mcbond_other5.6917.2711074
X-RAY DIFFRACTIONr_mcangle_it8.19910.8571335
X-RAY DIFFRACTIONr_mcangle_other8.20210.8661336
X-RAY DIFFRACTIONr_scbond_it6.7388.1031208
X-RAY DIFFRACTIONr_scbond_other6.7048.0961206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.49411.8131717
X-RAY DIFFRACTIONr_long_range_B_refined13.04183.6432638
X-RAY DIFFRACTIONr_long_range_B_other13.04383.6622637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.296→2.356 Å
RfactorNum. reflection% reflection
Rfree0.427 55 3.8 %
Rwork0.388 1386 -
obs--97.43 %

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