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- PDB-1wu3: Crystal structure of recombinant murine interferon beta -

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Basic information

Entry
Database: PDB / ID: 1wu3
TitleCrystal structure of recombinant murine interferon beta
ComponentsInterferon beta
KeywordsCYTOKINE / alpha-helix-bundle
Function / homology
Function and homology information


negative regulation of Lewy body formation / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / Interferon alpha/beta signaling / cellular response to dsRNA / type I interferon-mediated signaling pathway / response to exogenous dsRNA / negative regulation of osteoclast differentiation / humoral immune response / B cell proliferation ...negative regulation of Lewy body formation / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / Interferon alpha/beta signaling / cellular response to dsRNA / type I interferon-mediated signaling pathway / response to exogenous dsRNA / negative regulation of osteoclast differentiation / humoral immune response / B cell proliferation / cellular response to dexamethasone stimulus / positive regulation of autophagy / cytokine activity / neuron cellular homeostasis / cellular response to virus / defense response to virus / adaptive immune response / defense response to bacterium / 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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsSenda, T. / Saitoh, S. / Mitsui, Y.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined crystal structure of recombinant murine interferon-beta at 2.15 A resolution
Authors: Senda, T. / Saitoh, S. / Mitsui, Y.
#1: 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.
#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: Pharmacol.Ther. / Year: 1993
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.
History
DepositionDec 1, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 14, 2004ID: 1RMI
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_residues
Revision 1.4Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
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
I: Interferon beta


Theoretical massNumber of molelcules
Total (without water)19,7611
Polymers19,7611
Non-polymers00
Water86548
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 / IFN-beta


Mass: 19760.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01575
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: Ammonium Sulfate, dioxane, acetate buffer, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 7, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 22157 / Num. obs: 14666 / % possible obs: 66.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.18 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.8→1.88 Å / % possible all: 12.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
WEISdata reduction
SCALEdata scaling
PROTEINSYSTEM (PROF. Y. MITSUI)phasing
RefinementMethod to determine structure: MIR / Resolution: 2.15→7.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.918 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24731 1182 10.1 %RANDOM
Rwork0.19162 ---
all0.1973 10525 --
obs0.1973 10525 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.15→7.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 48 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221412
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.941899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1815159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76323.55376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.31513
X-RAY DIFFRACTIONr_chiral_restr0.0930.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021044
X-RAY DIFFRACTIONr_nbd_refined0.2270.2671
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.21
X-RAY DIFFRACTIONr_mcbond_it1.8481.5819
X-RAY DIFFRACTIONr_mcangle_it2.42521300
X-RAY DIFFRACTIONr_scbond_it3.1453680
X-RAY DIFFRACTIONr_scangle_it4.844.5599
LS refinement shellResolution: 2.15→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 81 -
Rwork0.345 604 -
obs--100 %

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