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- PDB-8idx: Structure of p205 HIN -

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Basic information

Entry
Database: PDB / ID: 8idx
TitleStructure of p205 HIN
ComponentsInterferon-activable protein 205-B
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / monocyte differentiation / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / negative regulation of innate immune response / activation of innate immune response / Neutrophil degranulation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / monocyte differentiation / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / negative regulation of innate immune response / activation of innate immune response / Neutrophil degranulation / nuclear periphery / positive regulation of interleukin-1 beta production / cellular response to ionizing radiation / double-stranded DNA binding / defense response to virus / nuclear speck / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Interferon-activable protein 205-B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, Y.L. / Jin, T.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to Be published
Title: Structure of p205 HIN
Authors: Li, Y.L. / Jin, T.C.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-activable protein 205-B
B: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,49134
Polymers49,1082
Non-polymers2,38332
Water3,765209
1
A: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,80319
Polymers24,5541
Non-polymers1,24918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-activable protein 205-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,68715
Polymers24,5541
Non-polymers1,13314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.638, 51.121, 56.578
Angle α, β, γ (deg.)103.15, 105.17, 108.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Interferon-activable protein 205-B / Ifi-205-B / Interferon-inducible protein p205-B / Myeloid cell nuclear differentiation antigen / Protein D3


Mass: 24553.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mnda, Ifi205b / Plasmid: PET30a / Details (production host): MBP tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DOV1
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 25% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→29.546 Å / Num. obs: 158200 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.02271 / Rpim(I) all: 0.01421 / Rrim(I) all: 0.02688 / Net I/σ(I): 28.96
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2504 / Num. unique obs: 15198 / CC1/2: 0.969 / CC star: 0.992 / Rrim(I) all: 0.2991 / % possible all: 94.55

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459: ???)refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.546 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2277 5.01 %
Rwork0.1725 --
obs0.1738 45448 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 155 209 3430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063257
X-RAY DIFFRACTIONf_angle_d0.7654323
X-RAY DIFFRACTIONf_dihedral_angle_d6.9071930
X-RAY DIFFRACTIONf_chiral_restr0.056478
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.78830.30881400.23862609X-RAY DIFFRACTION93
1.7883-1.82990.30461480.22642685X-RAY DIFFRACTION95
1.8299-1.87560.24921340.20612669X-RAY DIFFRACTION95
1.8756-1.92630.28321400.21222629X-RAY DIFFRACTION95
1.9263-1.9830.20491460.19112691X-RAY DIFFRACTION96
1.983-2.0470.26331440.19352713X-RAY DIFFRACTION96
2.047-2.12010.23171350.2042673X-RAY DIFFRACTION95
2.1201-2.2050.22411480.19022710X-RAY DIFFRACTION96
2.205-2.30530.22561340.19782705X-RAY DIFFRACTION96
2.3053-2.42680.2491490.19892707X-RAY DIFFRACTION97
2.4268-2.57880.21441400.19322743X-RAY DIFFRACTION97
2.5788-2.77770.21741390.18682713X-RAY DIFFRACTION97
2.7777-3.0570.22941480.18112736X-RAY DIFFRACTION97
3.057-3.49880.21631450.17192731X-RAY DIFFRACTION97
3.4988-4.40570.15911450.14592727X-RAY DIFFRACTION97
4.4057-29.5460.15351420.14892730X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 7.2558 Å / Origin y: -7.9458 Å / Origin z: 9.4848 Å
111213212223313233
T0.2389 Å2-0.0702 Å20.0138 Å2-0.2609 Å2-0.0056 Å2--0.233 Å2
L0.2932 °2-0.2757 °2-0.0492 °2-2.8463 °20.7125 °2--0.9372 °2
S-0.037 Å °0.0193 Å °0.0286 Å °0.0238 Å °0.0912 Å °0.0281 Å °-0.0652 Å °0.0594 Å °-0.0504 Å °
Refinement TLS groupSelection details: all

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