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- PDB-6rg1: Photorhabdus laumondii lectin PLL2 in complex with L-rhamnose -

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Basic information

Entry
Database: PDB / ID: 6rg1
TitlePhotorhabdus laumondii lectin PLL2 in complex with L-rhamnose
Componentslectin PLL2 from Photorhabdus laumondii
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / l-rhamnose / beta-propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / ACETATE ION / beta-L-rhamnopyranose / 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: 1.7 Å
AuthorsHouser, J. / Fujdiarova, E. / Wimmerova, M.
CitationJournal: Febs J. / Year: 2021
Title: Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system.
Authors: Fujdiarova, E. / Houser, J. / Dobes, P. / Paulikova, G. / Kondakov, N. / Kononov, L. / Hyrsl, P. / Wimmerova, M.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 24, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin PLL2 from Photorhabdus laumondii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,86915
Polymers40,1511
Non-polymers71814
Water6,666370
1
A: lectin PLL2 from Photorhabdus laumondii
hetero molecules

A: lectin PLL2 from Photorhabdus laumondii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,73930
Polymers80,3022
Non-polymers1,43728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5880 Å2
ΔGint-93 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.066, 71.003, 85.764
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein lectin PLL2 from Photorhabdus laumondii


Mass: 40150.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu0734 / Plasmid: pET25-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: Q7N8I8
#4: Sugar ChemComp-RM4 / beta-L-rhamnopyranose / beta-L-rhamnose / 6-deoxy-beta-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-rhamnopyranoseCOMMON NAMEGMML 1.0
b-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 383 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 8% PEG 4000, 150 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→47.11 Å / Num. obs: 41015 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.416 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.133 / Net I/σ(I): 4.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5990 / CC1/2: 0.519 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.672 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20945 2004 4.9 %RANDOM
Rwork0.18146 ---
obs0.1828 38688 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å21.07 Å2
2---1.11 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 45 370 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172376
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6183794
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5685481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0965346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64922.411141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96515370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2521515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6991.91375
X-RAY DIFFRACTIONr_mcbond_other0.6841.8931368
X-RAY DIFFRACTIONr_mcangle_it1.092.8371711
X-RAY DIFFRACTIONr_mcangle_other1.092.8381712
X-RAY DIFFRACTIONr_scbond_it0.8171.9691386
X-RAY DIFFRACTIONr_scbond_other0.8171.9711387
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3242.9312081
X-RAY DIFFRACTIONr_long_range_B_refined4.29924.0363447
X-RAY DIFFRACTIONr_long_range_B_other3.97223.2453342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 159 -
Rwork0.295 2866 -
obs--98.73 %

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