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- PDB-1d9c: BOVINE INTERFERON-GAMMA AT 2.0 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1d9c
TitleBOVINE INTERFERON-GAMMA AT 2.0 ANGSTROMS
ComponentsINTERFERON-GAMMA
KeywordsIMMUNE SYSTEM / helical homodimer
Function / homology
Function and homology information


Interferon gamma signaling / Regulation of IFNG signaling / IFNG signaling activates MAPKs / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of vitamin D biosynthetic process / type III interferon-mediated signaling pathway / positive regulation of interleukin-23 production ...Interferon gamma signaling / Regulation of IFNG signaling / IFNG signaling activates MAPKs / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of vitamin D biosynthetic process / type III interferon-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of smooth muscle cell apoptotic process / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / cell surface receptor signaling pathway via STAT / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / positive regulation of amyloid-beta formation / Fc-gamma receptor signaling pathway involved in phagocytosis / humoral immune response / macrophage differentiation / positive regulation of epithelial cell migration / type II interferon-mediated signaling pathway / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / regulation of insulin secretion / cytokine activity / astrocyte activation / positive regulation of protein-containing complex assembly / negative regulation of smooth muscle cell proliferation / microglial cell activation / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / defense response to virus / adaptive immune response / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Interferon gamma / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRandal, M. / Kossiakoff, A.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species.
Authors: Randal, M. / Kossiakoff, A.A.
History
DepositionOct 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: INTERFERON-GAMMA
B: INTERFERON-GAMMA


Theoretical massNumber of molelcules
Total (without water)28,5112
Polymers28,5112
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-49 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.150, 81.080, 83.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe asymmetric unit contains the biologically relevant homodimer

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Components

#1: Protein INTERFERON-GAMMA


Mass: 14255.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P07353
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, sodium chloride, sodium citrate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 39 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 50 %sat / Common name: sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. all: 16274 / Num. obs: 71885 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 72.5
Reflection shellResolution: 2.02→2.07 Å / % possible all: 86.5
Reflection
*PLUS
Num. obs: 16274 / Num. measured all: 71855
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
XDSdata reduction
AUTOMARdata reduction
RefinementResolution: 2→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 349992.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: NCS restraints were applied to individual helices, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1612 10 %random
Rwork0.201 ---
all0.21 16093 --
obs0.201 16093 96.1 %-
Solvent computationSolvent model: flat model / Bsol: 63.9842 Å2 / ksol: 0.341298 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 130 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_mcbond_it2.513.5
X-RAY DIFFRACTIONx_mcangle_it4.037
X-RAY DIFFRACTIONx_scbond_it6.435.5
X-RAY DIFFRACTIONx_scangle_it9.4914
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 183 8.9 %
Rwork0.29 1863 -
obs--72.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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