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- PDB-1ifa: THREE-DIMENSIONAL CRYSTAL STRUCTURE OF RECOMBINANT MURINE INTERFE... -

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Basic information

Entry
Database: PDB / ID: 1ifa
TitleTHREE-DIMENSIONAL CRYSTAL STRUCTURE OF RECOMBINANT MURINE INTERFERON-BETA
ComponentsINTERFERON-BETA
KeywordsGLYCOPROTEIN
Function / homology
Function and homology information


negative regulation of Lewy body formation / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / negative regulation of blood-brain barrier permeability / positive regulation of peptidyl-serine phosphorylation of STAT protein ...negative regulation of Lewy body formation / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / negative regulation of blood-brain barrier permeability / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of neuroinflammatory response / negative regulation of cell adhesion molecule production / positive regulation of transforming growth factor beta production / T cell activation involved in immune response / macrophage activation involved in immune response / cellular response to dsRNA / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / negative regulation of osteoclast differentiation / humoral immune response / negative regulation of type II interferon production / positive regulation of autophagy / B cell differentiation / cellular response to dexamethasone stimulus / cytokine activity / cellular response to virus / cytokine-mediated signaling pathway / neuron cellular homeostasis / defense response to virus / adaptive immune response / defense response to bacterium / negative regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Four-helical cytokine-like, core
Similarity search - Domain/homology
ASPARAGINE / Interferon beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMitsui, Y. / Senda, T. / Matsuda, S. / Kawano, G. / Nakamura, K.T. / Shimizu, H.
Citation
Journal: EMBO J. / Year: 1992
Title: Three-dimensional crystal structure of recombinant murine interferon-beta.
Authors: Senda, T. / Shimazu, T. / Matsuda, S. / Kawano, G. / Shimizu, H. / Nakamura, K.T. / Mitsui, Y.
#1: Journal: To be Published
Title: Structural, Functional and Evolutionary Implications of the Three-Dimensional Crystal Structure of Murine Interferon-Beta
Authors: Mitsui, Y. / Senda, T. / Shimazu, T. / Matsuda, S. / Utsumi, J.
#2: Journal: Proc.Jpn.Acad.,Ser.B / Year: 1990
Title: Three-Dimensional Structure of Recombinant Murine Interferon-Beta
Authors: Senda, T. / Matsuda, S. / Kurihara, H. / Nakamura, K.T. / Kawano, G. / Shimizu, H. / Mizuno, H. / Mitsui, Y.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: New Crystal Form of Recombinant Murine Interferon-Beta
Authors: Matsuda, S. / Senda, T. / Itoh, S. / Kawano, G. / Mizuno, H. / Mitsui, Y.
History
DepositionOct 29, 1991Processing 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 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 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-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5522
Polymers19,4201
Non-polymers1321
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.400, 71.400, 79.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein INTERFERON-BETA / Coordinate model: Cα atoms only


Mass: 19419.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01575
#2: Chemical ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
Compound detailsAS DEDUCED FROM GENE-MANIPULATING EXPERIMENTS ON THE INTERFERON-ALPHA THE FUNCTIONALLY IMPORTANT ...AS DEDUCED FROM GENE-MANIPULATING EXPERIMENTS ON THE INTERFERON-ALPHA THE FUNCTIONALLY IMPORTANT POLYPEPTIDE SEGMENTS ARE ON THE LOOP AB, ON THE HELIX D, AND ON THE LOOP DE. THESE SEGMENTS ARE SPATIALLY CLOSE TO EACH OTHER AND FORM A HOT AREA WHICH IS MOST PROBABLY THE BINDING SITE TO THE COGNATE RECEPTORS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 5.3 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
20.02 %sodium azide1drop
314 %dioxane1drop1.0 micro litter
420 %satammonium sulfate1reservoir
550 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8045 / Num. measured all: 37143 / Rmerge(I) obs: 0.0668

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.205 / Rfactor obs: 0.205 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms158 0 1 0 159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Num. reflection obs: 5055 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.059

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