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- PDB-7fcj: Zebrafish SIGIRR TIR domain mutant - C299S -

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Basic information

Entry
Database: PDB / ID: 7fcj
TitleZebrafish SIGIRR TIR domain mutant - C299S
ComponentsSIGIRR protein
KeywordsIMMUNE SYSTEM / receptor protein
Function / homology
Function and homology information


negative regulation of inflammatory response / cell surface receptor signaling pathway / cell surface / plasma membrane
Similarity search - Function
Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWang, X. / Zhou, J.
CitationJournal: Iscience / Year: 2022
Title: Structural basis of the IL-1 receptor TIR domain-mediated IL-1 signaling
Authors: Zhou, J. / Xiao, Y. / Ren, Y. / Ge, J. / Wang, X.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGIRR protein


Theoretical massNumber of molelcules
Total (without water)18,4031
Polymers18,4031
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7920 Å2
Unit cell
Length a, b, c (Å)31.744, 61.612, 69.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SIGIRR protein


Mass: 18403.182 Da / Num. of mol.: 1 / Mutation: C299S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: sigirr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K9K3G6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.85 Å3/Da / Density % sol: 33.41 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 10663 / % possible obs: 91.83 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 631

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FCC

7fcc


Resolution: 1.88→46.11 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 522 4.9 %
Rwork0.1977 10135 -
obs0.1997 10657 91.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.71 Å2 / Biso mean: 23.5894 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.88→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 0 105 1330
Biso mean---31.55 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-2.070.34731090.25181884199370
2.07-2.370.24661210.20742602272396
2.37-2.980.2651420.209227632905100
2.98-46.110.20561500.179928863036100

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