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- PDB-4l5t: Crystal structure of the tetrameric p202 HIN2 -

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Basic information

Entry
Database: PDB / ID: 4l5t
TitleCrystal structure of the tetrameric p202 HIN2
ComponentsInterferon-activable protein 202
KeywordsIMMUNE SYSTEM / HIN200 / OB-fold / tetramerization / DNA BINDING PROTEIN
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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response ...negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response / nucleolus / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / 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 / molecular replacement / Resolution: 3.405 Å
AuthorsYin, Q. / Tian, Y. / Wu, H.
CitationJournal: Cell Rep / Year: 2013
Title: Molecular Mechanism for p202-Mediated Specific Inhibition of AIM2 Inflammasome Activation.
Authors: Yin, Q. / Sester, D.P. / Tian, Y. / Hsiao, Y.S. / Lu, A. / Cridland, J.A. / Sagulenko, V. / Thygesen, S.J. / Choubey, D. / Hornung, V. / Walz, T. / Stacey, K.J. / Wu, H.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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
C: Interferon-activable protein 202
D: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)92,5534
Polymers92,5534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-activable protein 202
C: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)46,2772
Polymers46,2772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area16950 Å2
MethodPISA
3
A: Interferon-activable protein 202
D: Interferon-activable protein 202


Theoretical massNumber of molelcules
Total (without water)46,2772
Polymers46,2772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-10 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.892, 71.860, 95.465
Angle α, β, γ (deg.)90.000, 102.380, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimer of dimers

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Components

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


Mass: 23138.256 Da / Num. of mol.: 4 / Fragment: p202 HIN2, UNP residues 244-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Czech II / Gene: Ifi202, Ifi202a, Ifi202b / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: Q9R002

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22-25% PEG 3350, 0.1 M Tris pH 8.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2012
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 14.54 / Number: 75488 / Rmerge(I) obs: 0.21 / Χ2: 1.31 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 11186 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.32509810.1163.8646.6
5.817.3298.810.1621.7396.7
5.085.8199.510.1811.4187.1
4.615.0897.410.1751.3856.4
4.284.6198.910.1971.176.9
4.034.2899.110.2720.9597
3.834.0399.310.3930.7067.1
3.663.8397.310.4790.6526.3
3.523.669910.6370.5676.6
3.43.5298.610.8720.5256.8
ReflectionResolution: 3.4→50 Å / Num. all: 11345 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.21 / Χ2: 1.306 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.4-3.526.80.87210750.525198.6
3.52-3.666.60.63711350.567199
3.66-3.836.30.47910850.652197.3
3.83-4.037.10.39311010.706199.3
4.03-4.2870.27211380.959199.1
4.28-4.616.90.19711171.17198.9
4.61-5.086.40.17511051.385197.4
5.08-5.817.10.18111291.418199.5
5.81-7.326.70.16211421.739198.8
7.32-506.60.11611593.864198

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å46.39 Å
Translation3.5 Å46.39 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.4.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB IDs 2OQ0 and 3B6Y

2oq0

3b6y


Resolution: 3.405→46.388 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7903 / SU ML: 0.51 / σ(F): 1.41 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 2147 9.99 %Random
Rwork0.206 ---
all0.2355 21948 --
obs0.2122 21483 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.87 Å2 / Biso mean: 102.8334 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.405→46.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 0 0 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075858
X-RAY DIFFRACTIONf_angle_d1.1197891
X-RAY DIFFRACTIONf_chiral_restr0.077886
X-RAY DIFFRACTIONf_plane_restr0.003986
X-RAY DIFFRACTIONf_dihedral_angle_d14.6642105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4052-3.48430.3621360.27721185132194
3.4843-3.57140.31781480.23591333148199
3.5714-3.6680.31721440.22721307145199
3.668-3.77590.33621400.22431259139995
3.7759-3.89770.29021420.21811275141798
3.8977-4.03690.29151420.20651286142899
4.0369-4.19840.20811470.20331323147099
4.1984-4.38940.24751430.20161296143999
4.3894-4.62060.29351470.17751321146899
4.6206-4.90980.22561410.17351275141698
4.9098-5.28840.22221460.17621296144297
5.2884-5.81970.24421460.22341301144799
5.8197-6.65970.29471470.21921312145999
6.6597-8.38240.27571450.20951281142697
8.3824-46.39250.2541330.20291286141996

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