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- PDB-4jbj: Structural mimicry for functional antagonism -

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Basic information

Entry
Database: PDB / ID: 4jbj
TitleStructural mimicry for functional antagonism
ComponentsInterferon-activable protein 202
KeywordsDNA BINDING PROTEIN / OB fold / ds DNA
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response ...negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response / nucleus / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Interferon-activable protein 202
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 Å
AuthorsRu, H. / Ni, X. / Ma, F. / Zhao, L. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
CitationJournal: Cell Res. / Year: 2013
Title: Structural basis for termination of AIM2-mediated signaling by p202
Authors: Ru, H. / Ni, X. / Zhao, L. / Crowley, C. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-activable protein 202
B: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)45,4102
Polymers45,4102
Non-polymers00
Water61334
1
A: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)22,7051
Polymers22,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)22,7051
Polymers22,7051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.949, 70.749, 76.823
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Interferon-activable protein 202 / Ifi-202 / Interferon-inducible protein p202 / Lupus susceptibility protein p202


Mass: 22705.160 Da / Num. of mol.: 2 / Fragment: HINa domain, UNP residues 42-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifi202a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R002
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUECE WAS CAUSED BY STRAIN AKR.

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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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.05M Bis-Tris, 30%(v/v) pentaerythritol ethoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.692→50 Å / Num. all: 17603 / Num. obs: 17058 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBM

4jbm


Resolution: 2.692→35.374 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7571 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1689 9.9 %RANDOM
Rwork0.2288 ---
all0.231 17603 --
obs0.2331 17058 96.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.17 Å2 / Biso mean: 68.2579 Å2 / Biso min: 31.37 Å2
Refinement stepCycle: LAST / Resolution: 2.692→35.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 34 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043223
X-RAY DIFFRACTIONf_angle_d0.9754320
X-RAY DIFFRACTIONf_chiral_restr0.066479
X-RAY DIFFRACTIONf_plane_restr0.004543
X-RAY DIFFRACTIONf_dihedral_angle_d13.5761232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6921-2.77130.34871280.27681151127988
2.7713-2.86070.34861410.28631290143197
2.8607-2.96290.35481420.27671285142797
2.9629-3.08140.40241400.27531278141898
3.0814-3.22160.27251440.26781276142098
3.2216-3.39130.29881320.25491304143698
3.3913-3.60360.28751420.23141292143498
3.6036-3.88150.29611560.2251286144298
3.8815-4.27150.24531470.20651281142897
4.2715-4.88830.22331340.17871301143597
4.8883-6.15340.22721380.20221263140194
6.1534-35.37750.2151450.22341362150799
Refinement TLS params.Method: refined / Origin x: 19.8675 Å / Origin y: 7.0159 Å / Origin z: 95.4815 Å
111213212223313233
T0.3647 Å20.0188 Å20.0286 Å2-0.3681 Å20.0236 Å2--0.3867 Å2
L-0.0311 °20.0299 °20.076 °2-0.0064 °20.1032 °2--0.7072 °2
S0.0199 Å °-0.0085 Å °-0.0179 Å °-0.0583 Å °0.0457 Å °-0.0221 Å °-0.1186 Å °-0.1314 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 199
2X-RAY DIFFRACTION1ALLB2 - 199
3X-RAY DIFFRACTION1ALLA201 - 219
4X-RAY DIFFRACTION1ALLB201 - 215

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