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- PDB-8q7u: Photorhabdus laumondii lectin PLL in complex with alpha-methyl-fu... -

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Basic information

Entry
Database: PDB / ID: 8q7u
TitlePhotorhabdus laumondii lectin PLL 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) / metal ion binding / methyl 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: 1.6 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)41,7054
Polymers41,2421
Non-polymers4623
Water5,693316
1
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)166,82016
Polymers164,9704
Non-polymers1,85012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11300 Å2
ΔGint-13 kcal/mol
Surface area44560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.217, 89.184, 158.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

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Components

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


Mass: 41242.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0732 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q7N8J0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: 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.: 2 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7.5 / Details: 20 mM Tris/HCl 150 mM NaCl

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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 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→45.555 Å / Num. obs: 66905 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 9679 / CC1/2: 0.828 / Rpim(I) all: 0.288 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.555 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.265 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1796 3371 5.039 %
Rwork0.1625 63532 -
all0.163 --
obs-66903 99.981 %
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: 18.573 Å2
Baniso -1Baniso -2Baniso -3
1-1.048 Å2-0 Å2-0 Å2
2---0.381 Å20 Å2
3----0.667 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 31 316 3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0112970
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162640
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6214108
X-RAY DIFFRACTIONr_angle_other_deg0.6181.5696070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0685393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.302515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5210426
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.74610131
X-RAY DIFFRACTIONr_chiral_restr0.0950.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023603
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02757
X-RAY DIFFRACTIONr_nbd_refined0.1840.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22366
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21439
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2195
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.26
X-RAY DIFFRACTIONr_nbd_other0.1590.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.225
X-RAY DIFFRACTIONr_mcbond_it2.0211.8791476
X-RAY DIFFRACTIONr_mcbond_other2.0211.8791476
X-RAY DIFFRACTIONr_mcangle_it2.773.3751865
X-RAY DIFFRACTIONr_mcangle_other2.7743.3761866
X-RAY DIFFRACTIONr_scbond_it2.7472.0671494
X-RAY DIFFRACTIONr_scbond_other2.7462.0671495
X-RAY DIFFRACTIONr_scangle_it4.0153.6792231
X-RAY DIFFRACTIONr_scangle_other4.0143.6782232
X-RAY DIFFRACTIONr_lrange_it5.15119.4773431
X-RAY DIFFRACTIONr_lrange_other4.99518.293356
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
1.6-1.6420.252520.21646270.21848790.9570.9661000.193
1.642-1.6860.2122380.20445520.20447900.9680.9711000.179
1.686-1.7350.1842290.17744020.17746320.9750.97999.97840.153
1.735-1.7890.212270.17642650.17844920.9680.981000.151
1.789-1.8470.1922300.16241590.16343890.9750.9831000.138
1.847-1.9120.1962080.15840110.1642190.9740.9841000.135
1.912-1.9840.1992000.1538910.15240910.9760.9861000.13
1.984-2.0650.1722080.14837300.14939380.9820.9871000.13
2.065-2.1560.2041990.15135910.15437900.9750.9861000.133
2.156-2.2610.1511640.14334550.14336190.9860.9871000.125
2.261-2.3830.1641890.14332850.14434740.9830.9881000.128
2.383-2.5270.1811360.14331240.14432600.9810.9881000.13
2.527-2.7010.1711590.15129280.15230870.9830.9871000.139
2.701-2.9170.1741480.15927180.1628660.9820.9851000.15
2.917-3.1940.171350.17225300.17226650.9820.9831000.165
3.194-3.5690.1841320.19522940.19424260.980.9791000.19
3.569-4.1170.1861170.17420140.17521330.980.98399.90620.176
4.117-5.0320.14870.12917480.12918360.990.99199.94550.136
5.032-7.0730.208770.17413750.17514520.9820.9871000.178
7.073-45.5550.147360.1928330.198730.9870.97999.54180.197

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