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- PDB-4w8g: Crystal structure of the TIR domain of the Toll-related Receptor ... -

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Basic information

Entry
Database: PDB / ID: 4w8g
TitleCrystal structure of the TIR domain of the Toll-related Receptor TRR-2 from the lower metazoan Hydra magnipapillata (crystal form I)
ComponentsToll-receptor-related 2
KeywordsSIGNALING PROTEIN / Flavodoxin-like / Toll/Interleukin receptor TIR domain
Function / homology
Function and homology information


signal transduction / membrane
Similarity search - Function
Tetratricopeptide repeat protein 22 / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll-receptor-related 2
Similarity search - Component
Biological speciesHydra vulgaris (swiftwater hydra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWeisse, R.H.-J. / Scheidig, A.J.
CitationJournal: To Be Published
Title: Crystal structure of the TIR domain of the Toll-related Receptor TRR-2 from the lower metazoan Hydra magnipapillata (crystal form I)
Authors: Scheidig, A.J. / Weisse, R.H.-J.
History
DepositionAug 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-receptor-related 2


Theoretical massNumber of molelcules
Total (without water)16,1591
Polymers16,1591
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.260, 33.510, 109.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Toll-receptor-related 2


Mass: 16159.447 Da / Num. of mol.: 1 / Fragment: UNP residues 95-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Gene: TRR-2 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus RIL / References: UniProt: A6M946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.21 % / Description: long, needle-like appearance
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM NaOAc buffer pH 5.6, 310 mM MgCl2, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.95→54.76 Å / Num. all: 9188 / Num. obs: 9188 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 7.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 9.8 % / Rmerge(I) obs: 5.035 / Mean I/σ(I) obs: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSMarch 30, 2013data reduction
XSCALENovember 3, 2014data scaling
Aimless0.3.11data scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated form of 1FYV

1fyv


Resolution: 1.95→54.755 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3019 444 4.86 %RANDOM
Rwork0.2498 ---
obs0.2522 9127 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→54.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 7 1050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061070
X-RAY DIFFRACTIONf_angle_d1.2161456
X-RAY DIFFRACTIONf_dihedral_angle_d13.328395
X-RAY DIFFRACTIONf_chiral_restr0.059159
X-RAY DIFFRACTIONf_plane_restr0.008189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9502-2.23240.44571530.39412783X-RAY DIFFRACTION98
2.2324-2.81260.31481350.31392875X-RAY DIFFRACTION100
2.8126-54.77660.27511560.21193025X-RAY DIFFRACTION100

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