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- PDB-1rfb: CRYSTAL STRUCTURE OF RECOMBINANT BOVINE INTERFERON-GAMMA AT 3.0 A... -

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Basic information

Entry
Database: PDB / ID: 1rfb
TitleCRYSTAL STRUCTURE OF RECOMBINANT BOVINE INTERFERON-GAMMA AT 3.0 ANGSTROMS RESOLUTION
ComponentsINTERFERON-GAMMA
KeywordsGLYCOPROTEIN
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: 3 Å
AuthorsSamudzi, C.T. / Rubin, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of recombinant bovine interferon-gamma at 3.0 A resolution.
Authors: Samudzi, C.T. / Rubin, J.R.
History
DepositionJun 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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)28,1102
Polymers28,1102
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-40 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 79.900, 85.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SER B 19 - PRO B 20 OMEGA =279.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY B 26 - PRO B 27 OMEGA =290.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein INTERFERON-GAMMA


Mass: 14055.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P07353
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111.0 mg/mlprotein1drop
2100 mMammonium acetate1drop
330 %satammonium sulfate1drop
450 %satammonium sulphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.66 Å / Num. obs: 7891 / Num. measured all: 19800

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.192 / Rfactor obs: 0.192 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 43 2023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Num. reflection obs: 2744 / σ(I): 2 / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.052
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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