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- PDB-9ib7: Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondi... -

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Basic information

Entry
Database: PDB / ID: 9ib7
TitleTumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Blood group B trisaccharide
ComponentsPhotorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
KeywordsSUGAR BINDING PROTEIN / lectin / TNF-like / Photorhabdus laumondii / PLTL / fucose-binding
Function / homology: / Bc2l-C, N-terminal domain / alpha-L-fucopyranose / alpha-D-galactopyranose / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMelicher, F. / Wimmerova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
CitationJournal: Febs J. / Year: 2025
Title: Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.
Authors: Melicher, F. / Dobes, P. / Komarek, J. / Faltinek, L. / Korsak, M. / Sykorova, P. / Houser, J. / Wimmerova, M.
History
DepositionFeb 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1767
Polymers44,8553
Non-polymers1,3214
Water3,873215
1
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules

A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,35314
Polymers89,7106
Non-polymers2,6428
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18450 Å2
ΔGint-6 kcal/mol
Surface area27490 Å2
Unit cell
Length a, b, c (Å)81.823, 81.823, 112.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17


Mass: 14951.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu4240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MZP1
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: PEG1500, trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→46.474 Å / Num. obs: 61937 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Net I/σ(I): 25.5
Reflection shellResolution: 1.5→1.58 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8898 / CC1/2: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.474 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.364 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1989 3147 5.088 %
Rwork0.1743 58710 -
all0.176 --
obs-61857 99.992 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.319 Å2-0 Å2-0 Å2
2--0.319 Å2-0 Å2
3----0.638 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 89 215 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123322
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163041
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.7674589
X-RAY DIFFRACTIONr_angle_other_deg0.5961.77049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.126513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29710483
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.20810128
X-RAY DIFFRACTIONr_chiral_restr0.0880.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined0.1990.2490
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22754
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21664
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2143
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3950.219
X-RAY DIFFRACTIONr_nbd_other0.2290.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6160.213
X-RAY DIFFRACTIONr_mcbond_it1.9542.0211662
X-RAY DIFFRACTIONr_mcbond_other1.9432.0211662
X-RAY DIFFRACTIONr_mcangle_it2.6893.6282084
X-RAY DIFFRACTIONr_mcangle_other2.6893.6292085
X-RAY DIFFRACTIONr_scbond_it2.9932.3331660
X-RAY DIFFRACTIONr_scbond_other2.9922.3331661
X-RAY DIFFRACTIONr_scangle_it4.2764.1612485
X-RAY DIFFRACTIONr_scangle_other4.2754.1612486
X-RAY DIFFRACTIONr_lrange_it5.27920.8553509
X-RAY DIFFRACTIONr_lrange_other5.27820.8553510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2692090.23942850.2444940.9460.9611000.216
1.539-1.5810.2482380.21441560.21543940.9580.9691000.187
1.581-1.6270.2541990.19940520.20242510.9590.9731000.172
1.627-1.6770.2521860.19539770.19741630.9590.9751000.165
1.677-1.7320.2351960.18738260.18940220.9640.9771000.157
1.732-1.7920.2162180.17836870.1839050.970.981000.149
1.792-1.860.2272010.17335790.17637800.9670.9811000.145
1.86-1.9360.1982020.16834360.1736380.9750.9831000.144
1.936-2.0220.1871750.16933090.16934840.9790.9821000.145
2.022-2.120.1931750.1631650.16233400.9760.9841000.141
2.12-2.2350.1871790.16630160.16831950.9780.9831000.148
2.235-2.370.2321350.17428960.17730310.9680.9811000.156
2.37-2.5330.2061550.17626980.17828530.9740.9811000.16
2.533-2.7350.1881240.17825530.17826770.9770.981000.165
2.735-2.9950.2171320.17523200.17824530.9710.98199.95920.168
2.995-3.3470.1981060.17821430.17922490.9790.981000.174
3.347-3.8620.2011010.17319170.17520180.9740.9821000.178
3.862-4.7210.157930.14216130.14217070.9870.98999.94140.154
4.721-6.6430.164650.16113070.16113720.9870.9871000.178
6.643-46.4740.188580.2257750.2228330.9790.9641000.245

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