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- PDB-8q80: Photorhabdus laumondii lectin PLL2 in complex with alpha-methyl-f... -

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Basic information

Entry
Database: PDB / ID: 8q80
TitlePhotorhabdus laumondii lectin PLL2 in complex with alpha-methyl-fucoside
ComponentsPhotorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
KeywordsCELL ADHESION / lectin / saccharide binding protein / seven-bladed beta-propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / methyl alpha-L-fucopyranoside / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMelicher, F. / Houser, J. / Paulenova, E. / Wimmerova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic21-29622S Czech Republic
CitationJournal: Glycobiology / Year: 2025
Title: The insight into the biology of five homologous lectins produced by the entomopathogenic bacterium and nematode symbiont Photorhabdus laumondii.
Authors: Paulenova, E. / Dobes, P. / Melicher, F. / Houser, J. / Faltinek, L. / Hyrsl, P. / Wimmerova, M.
History
DepositionAug 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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 3/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5499
Polymers80,3022
Non-polymers1,2477
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-2 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.160, 85.676, 68.188
Angle α, β, γ (deg.)90.000, 102.062, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17


Mass: 40150.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0734 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q7N8I8
#2: Sugar
ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H14O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100 mM sodium acetate 11% PEG 4000

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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: 0.9799 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.85→85.68 Å / Num. obs: 64783 / % possible obs: 99.1 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Net I/σ(I): 11.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9343 / CC1/2: 0.785 / Rpim(I) all: 0.363 / Rrim(I) all: 0.729 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→66.683 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.828 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2296 3207 4.953 %
Rwork0.1968 61548 -
all0.198 --
obs-64755 98.961 %
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: 33.975 Å2
Baniso -1Baniso -2Baniso -3
1--1.132 Å20 Å20.41 Å2
2--2.857 Å20 Å2
3----1.741 Å2
Refinement stepCycle: LAST / Resolution: 1.85→66.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 84 144 5496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0115516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164873
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.6257593
X-RAY DIFFRACTIONr_angle_other_deg0.4881.56811143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.955684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.71528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25310728
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.37910246
X-RAY DIFFRACTIONr_chiral_restr0.0660.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021380
X-RAY DIFFRACTIONr_nbd_refined0.1820.2969
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24729
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22806
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.212
X-RAY DIFFRACTIONr_nbd_other0.1930.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.26
X-RAY DIFFRACTIONr_mcbond_it2.9383.3982742
X-RAY DIFFRACTIONr_mcbond_other2.9313.3982742
X-RAY DIFFRACTIONr_mcangle_it3.8626.0923424
X-RAY DIFFRACTIONr_mcangle_other3.8636.0933425
X-RAY DIFFRACTIONr_scbond_it3.223.6352774
X-RAY DIFFRACTIONr_scbond_other3.223.6362775
X-RAY DIFFRACTIONr_scangle_it4.6396.5574169
X-RAY DIFFRACTIONr_scangle_other4.6386.5574170
X-RAY DIFFRACTIONr_lrange_it5.97635.356352
X-RAY DIFFRACTIONr_lrange_other5.96935.2576339
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
1.85-1.8980.3552560.29444790.29748220.9080.92598.19580.278
1.898-1.950.292490.26843460.26946690.9290.94298.41510.251
1.95-2.0060.2551830.24143520.24246030.9570.95698.52270.225
2.006-2.0680.252000.23141800.23244460.9560.96398.51550.215
2.068-2.1360.2681890.22440330.22642820.9520.96798.59880.207
2.136-2.2110.2742050.22638800.22841380.9520.96798.71920.21
2.211-2.2940.2712460.21237050.21539960.9460.97198.87390.198
2.294-2.3880.2681720.19936790.20238880.9570.97599.04840.186
2.388-2.4940.2022310.18634500.18737230.9710.97898.87190.173
2.494-2.6150.2351570.19533630.19735520.9640.97899.09910.183
2.615-2.7570.2271440.20132080.20233720.970.97899.40690.19
2.757-2.9230.2691780.19929860.20231930.9580.97799.09180.192
2.923-3.1250.2911510.19828650.20230290.9520.97799.57080.196
3.125-3.3750.1941240.18726600.18827930.9750.97999.67780.187
3.375-3.6960.1871280.18724440.18725840.9770.97999.53560.19
3.696-4.130.1891160.17222140.17323390.9760.98199.61520.18
4.13-4.7660.1641140.15519670.15520880.9850.98799.66480.168
4.766-5.830.203780.17616700.17717550.9790.98599.60110.192
5.83-8.2140.283440.20413250.20613720.9560.97999.78130.218
8.214-66.6830.262420.237430.2327920.9320.96699.11620.237

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