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- PDB-8x70: The Crystal Structure of IFI16 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x70
TitleThe Crystal Structure of IFI16 from Biortus.
ComponentsGamma-interferon-inducible protein 16
KeywordsPROTEIN BINDING / Activator / DNA-binding / Apoptosis
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / STING mediated induction of host immune responses / myeloid cell differentiation / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / STING mediated induction of host immune responses / myeloid cell differentiation / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / activation of innate immune response / negative regulation of innate immune response / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / cellular response to ionizing radiation / autophagy / regulation of inflammatory response / double-stranded DNA binding / defense response to virus / regulation of autophagy / nuclear speck / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
BROMIDE ION / : / TRIETHYLENE GLYCOL / Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of IFI16 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Wang, J.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-interferon-inducible protein 16
B: Gamma-interferon-inducible protein 16
C: Gamma-interferon-inducible protein 16
D: Gamma-interferon-inducible protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,19725
Polymers94,1094
Non-polymers1,08821
Water14,268792
1
A: Gamma-interferon-inducible protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,96610
Polymers23,5271
Non-polymers4399
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gamma-interferon-inducible protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6063
Polymers23,5271
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gamma-interferon-inducible protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9588
Polymers23,5271
Non-polymers4317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gamma-interferon-inducible protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6684
Polymers23,5271
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.400, 87.418, 111.214
Angle α, β, γ (deg.)90.000, 99.274, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Gamma-interferon-inducible protein 16


Mass: 23527.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16666

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Non-polymers , 5 types, 813 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15M K bromide, 30% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18075 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18075 Å / Relative weight: 1
ReflectionResolution: 1.7→46.523 Å / Num. obs: 83684 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.798 / Num. unique obs: 4406

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.523 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.206 / SU B: 2.923 / SU ML: 0.095 / Average fsc free: 0.8906 / Average fsc work: 0.9098 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2472 4254 5.085 %
Rwork0.2007 79399 -
all0.203 --
obs-83653 99.798 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.443 Å20 Å2-1.388 Å2
2---0.783 Å20 Å2
3---0.754 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 45 792 7033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136335
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166310
X-RAY DIFFRACTIONr_angle_refined_deg1.331.6518492
X-RAY DIFFRACTIONr_angle_other_deg1.2281.58614610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4065761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91824.361305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.212151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3651522
X-RAY DIFFRACTIONr_chiral_restr0.0560.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
X-RAY DIFFRACTIONr_nbd_refined0.2310.21097
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26039
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23003
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.23213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2586
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2390.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3490.248
X-RAY DIFFRACTIONr_nbd_other0.2830.2193
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.244
X-RAY DIFFRACTIONr_mcbond_it1.6322.6673053
X-RAY DIFFRACTIONr_mcbond_other1.632.6673052
X-RAY DIFFRACTIONr_mcangle_it2.5633.9893805
X-RAY DIFFRACTIONr_mcangle_other2.5633.993806
X-RAY DIFFRACTIONr_scbond_it2.0632.9843282
X-RAY DIFFRACTIONr_scbond_other2.0632.9853283
X-RAY DIFFRACTIONr_scangle_it3.2874.3434685
X-RAY DIFFRACTIONr_scangle_other3.2874.3444686
X-RAY DIFFRACTIONr_lrange_it5.26532.5837001
X-RAY DIFFRACTIONr_lrange_other5.10132.0876827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3163270.2735844X-RAY DIFFRACTION99.8705
1.744-1.7920.3122950.265658X-RAY DIFFRACTION99.7152
1.792-1.8440.3083130.2415580X-RAY DIFFRACTION99.8306
1.844-1.9010.2582900.2265361X-RAY DIFFRACTION99.7177
1.901-1.9630.2933140.2225199X-RAY DIFFRACTION99.837
1.963-2.0320.2692640.2135064X-RAY DIFFRACTION99.9625
2.032-2.1080.2532310.2044930X-RAY DIFFRACTION99.8645
2.108-2.1950.2342660.1964657X-RAY DIFFRACTION99.8175
2.195-2.2920.2582380.1934539X-RAY DIFFRACTION99.7286
2.292-2.4040.2552230.1964293X-RAY DIFFRACTION99.735
2.404-2.5340.2891750.2054202X-RAY DIFFRACTION99.8403
2.534-2.6870.2622420.2083817X-RAY DIFFRACTION99.877
2.687-2.8730.2361640.2013677X-RAY DIFFRACTION99.5594
2.873-3.1030.2452070.2033384X-RAY DIFFRACTION99.6393
3.103-3.3990.2661750.2053121X-RAY DIFFRACTION99.8788
3.399-3.80.2521400.1962833X-RAY DIFFRACTION99.8992
3.8-4.3860.191260.1732532X-RAY DIFFRACTION99.7373
4.386-5.370.2251140.1682117X-RAY DIFFRACTION99.8657
5.37-7.5850.229960.211655X-RAY DIFFRACTION99.9429
7.585-46.5230.197540.198936X-RAY DIFFRACTION99.4975

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