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- PDB-9ib8: Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondi... -

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Basic information

Entry
Database: PDB / ID: 9ib8
TitleTumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Lewis Y tetrasaccharide
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 / 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: 1.6 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,2065
Polymers44,8553
Non-polymers1,3512
Water2,414134
1
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)92,41310
Polymers89,7106
Non-polymers2,7034
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area17990 Å2
ΔGint-2 kcal/mol
Surface area28500 Å2
Unit cell
Length a, b, c (Å)81.848, 81.848, 112.574
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)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 675.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 41.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: PEG1500, trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→46.38 Å / Num. obs: 51136 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 27.7
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 7323 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
SCALAdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40.958 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.636 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.203 2537 4.968 %
Rwork0.1799 48525 -
all0.181 --
obs-51062 99.941 %
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: 23.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.194 Å2-0 Å2-0 Å2
2--0.194 Å2-0 Å2
3----0.387 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 92 134 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123396
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163093
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.7664703
X-RAY DIFFRACTIONr_angle_other_deg0.6231.7027178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.401514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03210494
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.12110135
X-RAY DIFFRACTIONr_chiral_restr0.0910.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined0.1950.2517
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22887
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21710
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.21822
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.215
X-RAY DIFFRACTIONr_nbd_other0.2920.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.27
X-RAY DIFFRACTIONr_mcbond_it1.9752.2741704
X-RAY DIFFRACTIONr_mcbond_other1.9732.2741704
X-RAY DIFFRACTIONr_mcangle_it2.544.0822147
X-RAY DIFFRACTIONr_mcangle_other2.544.0842148
X-RAY DIFFRACTIONr_scbond_it3.1512.5981692
X-RAY DIFFRACTIONr_scbond_other3.152.5991693
X-RAY DIFFRACTIONr_scangle_it4.4774.6462534
X-RAY DIFFRACTIONr_scangle_other4.4764.6462535
X-RAY DIFFRACTIONr_lrange_it4.94423.1563554
X-RAY DIFFRACTIONr_lrange_other4.94423.1593555
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
1.6-1.6420.251960.21535090.21737050.9570.971000.192
1.642-1.6860.2361810.20234210.20436020.9660.9731000.176
1.686-1.7350.2281770.18133700.18435470.9670.9781000.156
1.735-1.7890.1981830.17832310.17934230.9750.97999.73710.151
1.789-1.8470.2231620.17731380.1833000.970.981000.15
1.847-1.9120.2291440.18330840.18532280.9650.9791000.157
1.912-1.9840.1911480.17529570.17631050.9760.9811000.152
1.984-2.0650.2221560.18328500.18530060.9680.9791000.161
2.065-2.1560.2371500.17127430.17428930.9660.9811000.154
2.156-2.2610.2291310.1826220.18327530.9730.981000.16
2.261-2.3830.2481330.19224960.19526290.9640.9781000.172
2.383-2.5270.2211200.1923900.19125180.9750.97999.68230.175
2.527-2.7010.2091110.19222260.19323370.970.9781000.18
2.701-2.9160.2061210.19121010.19222220.9710.9771000.183
2.916-3.1930.1941020.19219250.19220270.9770.9771000.188
3.193-3.5670.21900.19717840.19718740.9760.9781000.197
3.567-4.1130.193790.17515760.17616550.9810.9851000.181
4.113-5.0250.151620.13313550.13414220.9890.99199.64840.144
5.025-7.0540.158630.15710800.15711430.9860.9881000.169
7.054-40.9580.186280.2056670.2046990.9890.97299.42780.21

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