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- PDB-8q82: Photorhabdus laumondii lectin PLL4 in complex with alpha-methyl-f... -

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Basic information

Entry
Database: PDB / ID: 8q82
TitlePhotorhabdus laumondii lectin PLL4 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 / homologymethyl 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: 1.95 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

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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)81,74010
Polymers80,9082
Non-polymers8328
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-39 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.013, 82.859, 70.300
Angle α, β, γ (deg.)90.000, 105.357, 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: 40453.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0736 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8I6
#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.: 4 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG4000 20% PEG300 300 mM MgCl2 100 mM MES

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→46.28 Å / Num. obs: 56507 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.9999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 21.7
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 8229 / CC1/2: 0.978 / Rpim(I) all: 0.098 / Rrim(I) all: 0.251

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.464 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.77 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2399 2799 4.955 %
Rwork0.2046 53685 -
all0.206 --
obs-56484 99.897 %
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: 33.904 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.025 Å2
2--2.059 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 52 162 5440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0115470
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164763
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.6177537
X-RAY DIFFRACTIONr_angle_other_deg0.5321.59510903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2895674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.427524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26510721
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.31910258
X-RAY DIFFRACTIONr_chiral_restr0.0730.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021382
X-RAY DIFFRACTIONr_nbd_refined0.1770.2975
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.24616
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22730
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2810.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0760.22
X-RAY DIFFRACTIONr_nbd_other0.1930.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0510.27
X-RAY DIFFRACTIONr_mcbond_it3.1223.2922699
X-RAY DIFFRACTIONr_mcbond_other3.1223.2922699
X-RAY DIFFRACTIONr_mcangle_it4.1425.8963372
X-RAY DIFFRACTIONr_mcangle_other4.1435.8983373
X-RAY DIFFRACTIONr_scbond_it3.7263.6712771
X-RAY DIFFRACTIONr_scbond_other3.7263.6712772
X-RAY DIFFRACTIONr_scangle_it5.4116.5764165
X-RAY DIFFRACTIONr_scangle_other5.416.5764166
X-RAY DIFFRACTIONr_lrange_it6.55932.6386138
X-RAY DIFFRACTIONr_lrange_other6.54932.5186125
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
1.95-2.0010.321890.23239860.23641760.9330.96699.97610.213
2.001-2.0550.2581780.21638580.21840370.9520.97299.97520.2
2.055-2.1150.2651900.21437720.21639630.9490.97299.97480.196
2.115-2.180.2961690.21936450.22338140.9470.9691000.202
2.18-2.2510.2781700.20935360.21237060.9480.9731000.193
2.251-2.330.2751840.20434030.20835870.9590.9751000.188
2.33-2.4170.2631900.20832950.21134860.9620.97599.97130.194
2.417-2.5160.2411620.21231520.21433140.9650.9741000.202
2.516-2.6270.2581670.23430360.23632060.9620.9799.90640.225
2.627-2.7550.3091430.23828840.24130310.950.96899.8680.232
2.755-2.9030.2761690.22127750.22429480.9490.97199.86430.219
2.903-3.0780.2791600.2125810.21427440.9550.97399.89070.212
3.078-3.2890.2031360.224760.226140.9770.97799.92350.204
3.289-3.5510.2561050.20923130.21124190.9580.97699.95870.216
3.551-3.8870.1771010.18921410.18822470.9810.98199.77750.198
3.887-4.3410.1681080.16919150.16920250.9840.98499.90120.185
4.341-5.0040.161790.15817130.15817970.9840.98699.72180.179
5.004-6.1060.264900.21314110.21615090.9640.97799.46980.236
6.106-8.5430.294830.23511320.23912150.9550.9691000.259
8.543-41.4640.312260.2376610.246970.950.97198.56530.26

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