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- PDB-1eku: CRYSTAL STRUCTURE OF A BIOLOGICALLY ACTIVE SINGLE CHAIN MUTANT OF... -

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Basic information

Entry
Database: PDB / ID: 1eku
TitleCRYSTAL STRUCTURE OF A BIOLOGICALLY ACTIVE SINGLE CHAIN MUTANT OF HUMAN IFN-GAMMA
ComponentsInterferon gamma
KeywordsIMMUNE SYSTEM / CYTOKINE / PROTEIN ENGINEERING / INTERFERON
Function / homology
Function and homology information


positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process ...positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process / positive regulation of cellular respiration / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of interleukin-23 production / negative regulation of amyloid-beta clearance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of protein deacetylation / type III interferon-mediated signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of smooth muscle cell apoptotic process / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / positive regulation of killing of cells of another organism / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / positive regulation of MHC class II biosynthetic process / positive regulation of signaling receptor activity / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / negative regulation of epithelial cell differentiation / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / positive regulation of epithelial cell migration / positive regulation of nitric-oxide synthase biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / regulation of insulin secretion / humoral immune response / macrophage differentiation / positive regulation of autophagy / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of phagocytosis / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cytokine activity / astrocyte activation / negative regulation of smooth muscle cell proliferation / positive regulation of protein localization to plasma membrane / microglial cell activation / positive regulation of protein-containing complex assembly / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / positive regulation of protein import into nucleus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLandar, A. / Curry, B. / Parker, M.H. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Design, characterization, and structure of a biologically active single-chain mutant of human IFN-gamma.
Authors: Landar, A. / Curry, B. / Parker, M.H. / DiGiacomo, R. / Indelicato, S.R. / Nagabhushan, T.L. / Rizzi, G. / Walter, M.R.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_name_com.name / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.details
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0199
Polymers62,3472
Non-polymers6727
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-74 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.380, 111.380, 311.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-502-

SO4

21B-501-

SO4

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Components

#1: Protein Interferon gamma / IFN-gamma / Immune interferon


Mass: 31173.404 Da / Num. of mol.: 2 / Mutation: H111D, L121F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: T-CELLS, NK CELLS / Gene: IFNG / Production host: Escherichia coli (E. coli) / References: UniProt: P01579
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M NaCitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
35 mMbenzamidine1drop
41.4 Msodium citrate1reservoir
5100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 16757 / Num. obs: 16757 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.6 / Num. unique all: 1659 / % possible all: 100
Reflection
*PLUS
Num. measured all: 182491

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Processing

Software
NameVersionClassification
CNS0.4refinement
SCALEPACKdata scaling
RefinementResolution: 2.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 808 -RANDOM
Rwork0.246 ---
all0.251 16757 --
obs0.251 16183 95.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-12.381 Å20 Å2
2---1.44 Å20 Å2
3---2.881 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 35 2 4232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008008
X-RAY DIFFRACTIONc_angle_deg1.2289
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.749
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PARAM.WAT
X-RAY DIFFRACTION3PARAM.SO4
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.749

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