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- PDB-8q83: Photorhabdus laumondii lectin PLL5 in complex with alpha-methyl-f... -

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Basic information

Entry
Database: PDB / ID: 8q83
TitlePhotorhabdus laumondii lectin PLL5 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: 1.699 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
Revision 1.2Jul 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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


Theoretical massNumber of molelcules
Total (without water)163,90720
Polymers161,0564
Non-polymers2,85116
Water11,710650
1
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
D: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95310
Polymers80,5282
Non-polymers1,4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-6 kcal/mol
Surface area22520 Å2
MethodPISA
2
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95310
Polymers80,5282
Non-polymers1,4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-5 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.712, 102.940, 97.476
Angle α, β, γ (deg.)90.000, 90.028, 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: 40263.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0737 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8I5
#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.: 16 / 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.: 650 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: 20 mM Tris 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.6791
pseudo-merohedral22-h,-k,l20.3209
ReflectionResolution: 1.699→45.515 Å / Num. obs: 200282 / % possible obs: 98.8 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Net I/σ(I): 6.2
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 28794 / CC1/2: 0.466 / Rpim(I) all: 0.468 / Rrim(I) all: 0.917

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→45.515 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.906 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.018
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1997 10442 5.217 %
Rwork0.1823 189707 -
all0.183 --
obs-200149 98.503 %
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: 19.253 Å2
Baniso -1Baniso -2Baniso -3
1--5.193 Å2-0 Å21.795 Å2
2--1.938 Å20 Å2
3---3.256 Å2
Refinement stepCycle: LAST / Resolution: 1.699→45.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10562 0 192 650 11404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311130
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159709
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.63215307
X-RAY DIFFRACTIONr_angle_other_deg1.2281.60122195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53551374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85722.014561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.007151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4631560
X-RAY DIFFRACTIONr_chiral_restr0.0510.21462
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022863
X-RAY DIFFRACTIONr_nbd_refined0.170.21984
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.29717
X-RAY DIFFRACTIONr_nbtor_refined0.1630.25398
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.24615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2571
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.212
X-RAY DIFFRACTIONr_nbd_other0.2130.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.26
X-RAY DIFFRACTIONr_mcbond_it0.7952.0365493
X-RAY DIFFRACTIONr_mcbond_other0.7952.0365492
X-RAY DIFFRACTIONr_mcangle_it1.2233.0546859
X-RAY DIFFRACTIONr_mcangle_other1.2233.0546860
X-RAY DIFFRACTIONr_scbond_it0.7612.0885637
X-RAY DIFFRACTIONr_scbond_other0.7612.0885637
X-RAY DIFFRACTIONr_scangle_it1.1513.1178445
X-RAY DIFFRACTIONr_scangle_other1.1513.1178446
X-RAY DIFFRACTIONr_lrange_it2.27723.66412895
X-RAY DIFFRACTIONr_lrange_other2.20723.5612805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.699-1.7430.257240.21513617X-RAY DIFFRACTION95.7599
1.743-1.7910.2547510.2113373X-RAY DIFFRACTION96.9389
1.791-1.8430.2486890.21113371X-RAY DIFFRACTION98.5698
1.843-1.90.2457120.20712856X-RAY DIFFRACTION98.8705
1.9-1.9620.2396360.20312616X-RAY DIFFRACTION98.866
1.962-2.0310.2187370.19312102X-RAY DIFFRACTION98.9976
2.031-2.1070.2156960.19211623X-RAY DIFFRACTION99.0433
2.107-2.1930.1966230.18411056X-RAY DIFFRACTION97.2197
2.193-2.2910.1985580.17810922X-RAY DIFFRACTION99.1193
2.291-2.4030.2055690.18110368X-RAY DIFFRACTION98.9774
2.403-2.5330.1935460.1779900X-RAY DIFFRACTION99.6946
2.533-2.6860.1945380.1829319X-RAY DIFFRACTION99.3649
2.686-2.8710.2115610.1898546X-RAY DIFFRACTION97.5994
2.871-3.1010.1884560.1768214X-RAY DIFFRACTION99.7239
3.101-3.3970.2014060.1837614X-RAY DIFFRACTION99.7388
3.397-3.7970.23290.1836878X-RAY DIFFRACTION99.311
3.797-4.3830.163090.1625959X-RAY DIFFRACTION97.8
4.383-5.3660.1652920.1485143X-RAY DIFFRACTION99.9081
5.366-7.5770.1732220.1774003X-RAY DIFFRACTION99.6462
7.577-45.5150.198880.22227X-RAY DIFFRACTION96.7809

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