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- PDB-8q81: Photorhabdus laumondii lectin PLL3 in complex with alpha-methyl-f... -

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Basic information

Entry
Database: PDB / ID: 8q81
TitlePhotorhabdus laumondii lectin PLL3 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 / DI(HYDROXYETHYL)ETHER / 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: 1.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5149
Polymers40,5091
Non-polymers1,0058
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint20 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.611, 69.620, 76.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40509.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0735 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8I7
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 90 m HEPES, 9% PEG 8000

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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: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→76.25 Å / Num. obs: 48191 / % possible obs: 98.5 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.027 / Rrim(I) all: 0.101 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6850 / CC1/2: 0.897 / Rpim(I) all: 0.225 / Rrim(I) all: 0.83 / % possible all: 97.2

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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: 1.5→76.25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.32 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1868 2382 4.948 %
Rwork0.1603 45758 -
all0.162 --
obs-48140 98.331 %
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: 15.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.794 Å2-0 Å2-0 Å2
2---0.784 Å2-0 Å2
3---1.578 Å2
Refinement stepCycle: LAST / Resolution: 1.5→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 67 221 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0112830
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162473
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6313897
X-RAY DIFFRACTIONr_angle_other_deg0.5641.5955661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0425351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.32513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35810364
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.65310127
X-RAY DIFFRACTIONr_chiral_restr0.0820.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02720
X-RAY DIFFRACTIONr_nbd_refined0.1740.2451
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22329
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21427
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2182
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.24
X-RAY DIFFRACTIONr_nbd_other0.1710.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.221
X-RAY DIFFRACTIONr_mcbond_it1.4861.5071384
X-RAY DIFFRACTIONr_mcbond_other1.4861.5091385
X-RAY DIFFRACTIONr_mcangle_it2.212.7051735
X-RAY DIFFRACTIONr_mcangle_other2.2132.7071736
X-RAY DIFFRACTIONr_scbond_it2.2251.7011446
X-RAY DIFFRACTIONr_scbond_other2.2241.7021447
X-RAY DIFFRACTIONr_scangle_it3.2443.0222160
X-RAY DIFFRACTIONr_scangle_other3.2443.0232161
X-RAY DIFFRACTIONr_lrange_it4.2417.1753229
X-RAY DIFFRACTIONr_lrange_other4.15416.443183
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
1.5-1.5390.2371780.20732820.20835710.9580.96596.89160.185
1.539-1.5810.231640.18932180.19134880.9650.97296.9610.167
1.581-1.6270.1881480.18231360.18233730.9730.97597.36140.16
1.627-1.6770.2451560.18830300.19132650.9550.97497.58040.164
1.677-1.7320.2421300.16730260.1732300.9690.98197.7090.146
1.732-1.7930.2021630.15528610.15830870.9760.98497.95920.136
1.793-1.860.1721530.15527710.15629740.9830.98498.31880.138
1.86-1.9360.1851260.15327050.15428910.9770.98597.92460.135
1.936-2.0220.1871440.14926030.15127770.9790.98698.91970.134
2.022-2.120.1921150.15924790.16126390.9780.98598.29480.145
2.12-2.2350.1921470.15723500.15925200.9760.98599.08730.144
2.235-2.370.1691120.15622660.15724020.9820.98599.00080.144
2.37-2.5330.1551260.14720930.14822400.9840.98799.06250.137
2.533-2.7360.1481130.15120010.15121290.9870.98799.29540.141
2.736-2.9960.176920.15818420.15919440.9830.98599.48560.152
2.996-3.3480.171820.1616870.1617770.9790.98599.54980.158
3.348-3.8640.209880.16914850.17115760.9790.98399.80960.168
3.864-4.7250.155650.13512980.13613650.9890.9999.85350.14
4.725-6.6550.165490.16110060.16110560.9870.98899.90530.166
6.655-51.4120.315310.2086190.2136530.9440.96999.54060.207

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