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- PDB-5oem: Crystal Structure of Interferon Regulatory Factor 9 IAD Domain -

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Basic information

Entry
Database: PDB / ID: 5oem
TitleCrystal Structure of Interferon Regulatory Factor 9 IAD Domain
ComponentsInterferon regulatory factor 9Interferon regulatory factors
KeywordsTRANSCRIPTION / IRF9
Function / homology
Function and homology information


ISGF3 complex / Interferon alpha/beta signaling / immune system process / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Interferon regulatory factor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRengachari, S. / Panne, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function.
Authors: Rengachari, S. / Groiss, S. / Devos, J.M. / Caron, E. / Grandvaux, N. / Panne, D.
History
DepositionJul 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Interferon regulatory factor 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3382
Polymers21,2431
Non-polymers951
Water57632
1
A: Interferon regulatory factor 9
hetero molecules

A: Interferon regulatory factor 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6764
Polymers42,4862
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2170 Å2
ΔGint-26 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.770, 76.770, 85.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Interferon regulatory factor 9 / Interferon regulatory factors / IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon- ...IRF-9 / IFN-alpha-responsive transcription factor subunit / ISGF3 p48 subunit / Interferon-stimulated gene factor 3 gamma / ISGF-3 gamma / Transcriptional regulator ISGF3 subunit gamma


Mass: 21242.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf9, Isgf3g / Production host: Escherichia coli (E. coli) / References: UniProt: Q61179
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 6.8, 1.5 M Ammonium phosphate monobasic and 0.1 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.9→35.989 Å / Num. obs: 22803 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.923 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.041 / Χ2: 1.047 / Net I/σ(I): 14.81 / Num. measured all: 66645
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.012.3960.6561.4533140.8440.81588.3
2.01-2.153.0440.3773.1233950.9490.45696.8
2.15-2.323.1040.1795.9832740.9850.21598.8
2.32-2.542.9390.1019.2130050.9920.12398.8
2.54-2.843.1320.05815.7227450.9970.0799.4
2.84-3.283.0670.03824.6524300.9980.04598.9
3.28-4.012.8360.02633.7620610.9990.03298.2
4.01-5.643.0270.02240.3216180.9990.02797.9
5.64-35.9892.6880.02838.79610.9980.03496.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dsh

3dsh


Resolution: 1.9→35.989 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2421 1927 5.03 %
Rwork0.2069 --
obs0.2086 38295 85.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 297.71 Å2 / Biso mean: 76.8937 Å2 / Biso min: 32.89 Å2
Refinement stepCycle: final / Resolution: 1.9→35.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 5 32 1528
Biso mean--68.35 55.73 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141539
X-RAY DIFFRACTIONf_angle_d1.2632099
X-RAY DIFFRACTIONf_chiral_restr0.068226
X-RAY DIFFRACTIONf_plane_restr0.008280
X-RAY DIFFRACTIONf_dihedral_angle_d12.578930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.897-1.94450.3418930.37611815190860
1.9445-1.9970.34351170.33412191230871
1.997-2.05580.31051320.30552479261182
2.0558-2.12210.33051360.29252599273586
2.1221-2.1980.33131370.27572642277986
2.198-2.2860.32161440.25892625276988
2.286-2.390.29381390.25652679281888
2.39-2.5160.27761410.2522631277287
2.516-2.67360.26981430.24492692283588
2.6736-2.87990.28881430.22262789293292
2.8799-3.16960.24441480.22512796294493
3.1696-3.62780.24561440.20772768291291
3.6278-4.56920.21671540.16562813296793
4.5692-35.99570.19331560.17422849300593
Refinement TLS params.Method: refined / Origin x: 22.3049 Å / Origin y: 23.6272 Å / Origin z: 18.6301 Å
111213212223313233
T0.3054 Å20.041 Å2-0.0059 Å2-0.5231 Å20.0046 Å2--0.3016 Å2
L0.7357 °2-0.3581 °2-0.9006 °2-3.1148 °22.824 °2--5.2426 °2
S0.2634 Å °0.0553 Å °0.033 Å °-0.057 Å °-0.2498 Å °-0.0147 Å °-0.033 Å °-1.0026 Å °-0.0629 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA197 - 385
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 32

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