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

ID or keywords:

Entry

Database: PDB / ID: 8x70

Title

The Crystal Structure of IFI16 from Biortus.

Components

Gamma-interferon-inducible protein 16

Keywords

PROTEIN BINDING / Activator / DNA-binding / Apoptosis

Function / homology

Function and homology information

negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Wang, J.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of IFI16 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Wang, J.

History

Deposition	Nov 22, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x70.cif.gz	191.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8x70.ent.gz	144.1 KB	Display	PDB format
PDBx/mmJSON format	8x70.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x70_validation.pdf.gz	477.9 KB	Display	wwPDB validaton report
Full document	8x70_full_validation.pdf.gz	481 KB	Display
Data in XML	8x70_validation.xml.gz	37.6 KB	Display
Data in CIF	8x70_validation.cif.gz	55.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/8x70 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/8x70	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (3) #177 - Sep 2014 Apoptosomes similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #56 - Aug 2004 Caspases similarity (1) #224 - Aug 2018 Legumain similarity (1) #68 - Aug 2005 Neurotrophins similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

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

95.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gamma-interferon-inducible protein 16

hetero molecules

defined by author
Evidence: gel filtration
24 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gamma-interferon-inducible protein 16

hetero molecules

defined by author
23.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Gamma-interferon-inducible protein 16

hetero molecules

defined by author
24 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Gamma-interferon-inducible protein 16

hetero molecules

defined by author
23.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

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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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

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

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→46.523 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.938 / WR_factor R_free: 0.256 / WR_factor R_work: 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

	R_factor	Num. reflection	% reflection
R_free	0.2472	4254	5.085 %
R_work	0.2007	79399	-
all	0.203	-	-
obs	-	83653	99.798 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.626 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.443 Å²	0 Å²	-1.388 Å²
2-	-	-0.783 Å²	0 Å²
3-	-	-	0.754 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→46.523 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6196	0	45	792	7033

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	6335
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6310
X-RAY DIFFRACTION	r_angle_refined_deg	1.33	1.651	8492
X-RAY DIFFRACTION	r_angle_other_deg	1.228	1.586	14610
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.406	5	761
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.918	24.361	305
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.212	15	1292
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.365	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	860
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6907
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1341
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	1097
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	6039
X-RAY DIFFRACTION	r_nbtor_refined	0.155	0.2	3003
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	3213
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	586
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.02	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.239	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.349	0.2	48
X-RAY DIFFRACTION	r_nbd_other	0.283	0.2	193
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	44
X-RAY DIFFRACTION	r_mcbond_it	1.632	2.667	3053
X-RAY DIFFRACTION	r_mcbond_other	1.63	2.667	3052
X-RAY DIFFRACTION	r_mcangle_it	2.563	3.989	3805
X-RAY DIFFRACTION	r_mcangle_other	2.563	3.99	3806
X-RAY DIFFRACTION	r_scbond_it	2.063	2.984	3282
X-RAY DIFFRACTION	r_scbond_other	2.063	2.985	3283
X-RAY DIFFRACTION	r_scangle_it	3.287	4.343	4685
X-RAY DIFFRACTION	r_scangle_other	3.287	4.344	4686
X-RAY DIFFRACTION	r_lrange_it	5.265	32.583	7001
X-RAY DIFFRACTION	r_lrange_other	5.101	32.087	6827

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.744	0.316	327	0.273	5844	X-RAY DIFFRACTION	99.8705
1.744-1.792	0.312	295	0.26	5658	X-RAY DIFFRACTION	99.7152
1.792-1.844	0.308	313	0.241	5580	X-RAY DIFFRACTION	99.8306
1.844-1.901	0.258	290	0.226	5361	X-RAY DIFFRACTION	99.7177
1.901-1.963	0.293	314	0.222	5199	X-RAY DIFFRACTION	99.837
1.963-2.032	0.269	264	0.213	5064	X-RAY DIFFRACTION	99.9625
2.032-2.108	0.253	231	0.204	4930	X-RAY DIFFRACTION	99.8645
2.108-2.195	0.234	266	0.196	4657	X-RAY DIFFRACTION	99.8175
2.195-2.292	0.258	238	0.193	4539	X-RAY DIFFRACTION	99.7286
2.292-2.404	0.255	223	0.196	4293	X-RAY DIFFRACTION	99.735
2.404-2.534	0.289	175	0.205	4202	X-RAY DIFFRACTION	99.8403
2.534-2.687	0.262	242	0.208	3817	X-RAY DIFFRACTION	99.877
2.687-2.873	0.236	164	0.201	3677	X-RAY DIFFRACTION	99.5594
2.873-3.103	0.245	207	0.203	3384	X-RAY DIFFRACTION	99.6393
3.103-3.399	0.266	175	0.205	3121	X-RAY DIFFRACTION	99.8788
3.399-3.8	0.252	140	0.196	2833	X-RAY DIFFRACTION	99.8992
3.8-4.386	0.19	126	0.173	2532	X-RAY DIFFRACTION	99.7373
4.386-5.37	0.225	114	0.168	2117	X-RAY DIFFRACTION	99.8657
5.37-7.585	0.229	96	0.21	1655	X-RAY DIFFRACTION	99.9429
7.585-46.523	0.197	54	0.198	936	X-RAY DIFFRACTION	99.4975

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