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- PDB-4w8h: Crystal structure of the TIR domain of the Toll-related Receptor ... -

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Basic information

Entry
Database: PDB / ID: 4w8h
TitleCrystal structure of the TIR domain of the Toll-related Receptor TRR-2 from the lower metazoan Hydra magnipapillata (crystal form II)
Components
  • Toll-receptor-related 2
  • hexa-His tag
KeywordsSIGNALING PROTEIN / Flavodoxin-like / Toll/Interleukin receptor TIR domain
Function / homology
Function and homology information


toll-like receptor signaling pathway / transmembrane signaling receptor activity / immune response / membrane
Similarity search - Function
Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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 II)
Authors: Weisse, R.H.-J. / Scheidig, A.J.
History
DepositionAug 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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
D: hexa-His tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2133
Polymers16,1772
Non-polymers351
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-7 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.730, 63.570, 32.120
Angle α, β, γ (deg.)90.00, 105.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Toll-receptor-related 2


Mass: 15330.566 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: Protein/peptide hexa-His tag


Mass: 846.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus RIL
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.87 Å3/Da / Density % sol: 34.35 % / Description: short, needle-like appearance
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM NaOAc (pH 5;8), 350mM MgCl2, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918069 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918069 Å / Relative weight: 1
ReflectionResolution: 1.14→31.79 Å / Num. all: 42226 / Num. obs: 42226 / % possible obs: 97.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.1
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.659 / Mean I/σ(I) obs: 0.7 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSNovember 3, 2014data reduction
XSCALENovember 3, 2014data scaling
Aimless0.3.11data scaling
MOLREP11.0.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W8G

4w8g


Resolution: 1.14→31.785 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1714 2121 5.02 %RANDOM
Rwork0.14 ---
obs0.1417 42223 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→31.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 1 162 1260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131193
X-RAY DIFFRACTIONf_angle_d1.3641634
X-RAY DIFFRACTIONf_dihedral_angle_d12.359456
X-RAY DIFFRACTIONf_chiral_restr0.097175
X-RAY DIFFRACTIONf_plane_restr0.008214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.16650.3461420.32792583X-RAY DIFFRACTION96
1.1665-1.19570.30061400.29752626X-RAY DIFFRACTION95
1.1957-1.2280.29021250.27032650X-RAY DIFFRACTION96
1.228-1.26420.29631230.2512626X-RAY DIFFRACTION97
1.2642-1.3050.271390.22372649X-RAY DIFFRACTION96
1.305-1.35160.25591370.19572665X-RAY DIFFRACTION97
1.3516-1.40570.23591390.16812681X-RAY DIFFRACTION97
1.4057-1.46970.21321580.13512674X-RAY DIFFRACTION98
1.4697-1.54720.15771190.11672691X-RAY DIFFRACTION98
1.5472-1.64410.15581410.10672686X-RAY DIFFRACTION98
1.6441-1.77110.16281490.1012731X-RAY DIFFRACTION99
1.7711-1.94930.13991420.09952705X-RAY DIFFRACTION99
1.9493-2.23130.11161440.09592717X-RAY DIFFRACTION99
2.2313-2.81090.15771640.11562706X-RAY DIFFRACTION98
2.8109-31.79730.1411590.12782712X-RAY DIFFRACTION97

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