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- PDB-7fcl: Zebrafish SIGIRR TIR domain -

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Basic information

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


negative regulation of inflammatory response / cell surface / signal transduction / 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: 3.04 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 27, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGIRR protein
B: SIGIRR protein
C: SIGIRR protein


Theoretical massNumber of molelcules
Total (without water)55,2553
Polymers55,2553
Non-polymers00
Water00
1
A: SIGIRR protein
B: SIGIRR protein


Theoretical massNumber of molelcules
Total (without water)36,8372
Polymers36,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area15000 Å2
MethodPISA
2
C: SIGIRR protein

C: SIGIRR protein


Theoretical massNumber of molelcules
Total (without water)36,8372
Polymers36,8372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.996, 145.364, 75.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11C-299-

CYS

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 181 - 326 / Label seq-ID: 3 - 148

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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Components

#1: Protein SIGIRR protein


Mass: 18418.260 Da / Num. of mol.: 3 / Mutation: D218N
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
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH6.9, 34% v/v Pentaerythritol ethoxylate (15/4 EO/OH), 3% v/v Glycerol

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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: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 9184 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.1
Reflection shellResolution: 3.04→3.09 Å / Rmerge(I) obs: 0.689 / Num. unique obs: 455

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FCJ

7fcj


Resolution: 3.04→33.56 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 469 5.12 %
Rwork0.2388 8683 -
obs0.2408 9152 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.63 Å2 / Biso mean: 73.6809 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.04→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 0 3621
Num. residues----438
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1323X-RAY DIFFRACTION1.466TORSIONAL
12B1323X-RAY DIFFRACTION1.466TORSIONAL
13C1323X-RAY DIFFRACTION1.466TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.04-3.480.37111530.25882812296599
3.48-4.380.25361540.249128873041100
4.39-33.560.26051620.22692984314699

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