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- PDB-7ylg: Crystal structure of the chicken Toll-like receptor 15 TIR domain... -

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Basic information

Entry
Database: PDB / ID: 7ylg
TitleCrystal structure of the chicken Toll-like receptor 15 TIR domain (glutathione adduct)
ComponentsToll-like receptor 2
KeywordsIMMUNE SYSTEM / innate immune receptor
Function / homology
Function and homology information


toll-like receptor 2 signaling pathway / toll-like receptor signaling pathway / transmembrane signaling receptor activity / inflammatory response / innate immune response / membrane
Similarity search - Function
Toll-like receptor / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Toll-like receptor / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
GLUTATHIONE / Toll-like receptor 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKo, K.Y. / Song, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Iucrj / Year: 2023
Title: Structural analysis of the Toll-like receptor 15 TIR domain.
Authors: Ko, K.Y. / Song, W.S. / Park, J. / Lee, G.S. / Yoon, S.I.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: Toll-like receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0442
Polymers20,7371
Non-polymers3071
Water81145
1
A: Toll-like receptor 2
hetero molecules

A: Toll-like receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0884
Polymers41,4732
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3610 Å2
ΔGint-38 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.625, 64.625, 94.911
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1024-

HOH

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Components

#1: Protein Toll-like receptor 2


Mass: 20736.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli)
References: UniProt: H2D5F4, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Dipotassium hydrogen phosphate, sodium dihydrogen phosphate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 21418 / % possible obs: 97.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 0.996 / Net I/σ(I): 39.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1056 / CC1/2: 0.822 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YLF

7ylf


Resolution: 1.8→27.98 Å / SU ML: 0.2185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 1085 5.09 %
Rwork0.2137 20236 -
obs0.2151 21321 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 20 45 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871218
X-RAY DIFFRACTIONf_angle_d0.86741655
X-RAY DIFFRACTIONf_chiral_restr0.0609176
X-RAY DIFFRACTIONf_plane_restr0.0059209
X-RAY DIFFRACTIONf_dihedral_angle_d13.5623715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.33241200.29222543X-RAY DIFFRACTION99.37
1.88-1.980.30791480.26792509X-RAY DIFFRACTION99.25
1.98-2.110.29211470.22952492X-RAY DIFFRACTION98.8
2.11-2.270.26231460.22812520X-RAY DIFFRACTION98.67
2.27-2.50.24951520.22222528X-RAY DIFFRACTION98.28
2.5-2.860.28581280.23212523X-RAY DIFFRACTION98
2.86-3.60.23381240.21922560X-RAY DIFFRACTION96.86
3.6-27.980.20011200.18622561X-RAY DIFFRACTION93.25
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.57570802664-2.092309446580.2702667211232.05642891872-0.04558457243133.215464048840.00110032918136-0.475940645846-0.09686898774870.05446938144910.05033187970590.1190325598240.331161992719-0.362543077688-0.08166056915860.198310506256-0.04482146290790.006894451477270.2926507488810.04574806600720.21637094731312.477399992221.340338960713.869576043
22.87315587251-0.729452021335-2.570611676792.8638059072.568278535253.71132461099-0.118198623401-0.0326278594971-0.003807835925060.6438017518330.11486914536-0.0637751918565-0.1832103828620.0226305030497-0.0001662054786750.3766320026680.0514902117255-0.09671977678270.333002001947-0.005672420131140.33734531813818.206906350225.71865186042.02782806803
34.336913937131.339098627650.007069469178931.123512490411.059886750836.278859120880.1295352178050.033982879449-0.2914315163270.06034053684740.00563400319449-0.1935929811980.3147566166170.430696178117-0.1039223988630.2101142281890.0393202778963-0.07045915120760.299118732138-0.001342592495820.2919309990627.713656617419.55259988114.6982509226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 705 through 774 )
2X-RAY DIFFRACTION2chain 'A' and (resid 775 through 787 )
3X-RAY DIFFRACTION3chain 'A' and (resid 788 through 850 )

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