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- PDB-6rfz: Photorhabdus laumondii lectin PLL2 in complex with D-glucose -

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Basic information

Entry
Database: PDB / ID: 6rfz
TitlePhotorhabdus laumondii lectin PLL2 in complex with D-glucose
Componentslectin PLL2 from Photorhabdus laumondii
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / glucose / beta-propeller
Function / homology: / PLL-like beta propeller / Repeat of unknown function (DUF346) / ACETATE ION / beta-D-glucopyranose / 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: 1.8 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 ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)41,31113
Polymers40,1511
Non-polymers1,16012
Water6,503361
1
A: lectin PLL2 from Photorhabdus laumondii
hetero molecules

A: lectin PLL2 from Photorhabdus laumondii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,62226
Polymers80,3022
Non-polymers2,32024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6940 Å2
ΔGint-28 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.498, 71.099, 86.221
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

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Components

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Protein / Sugars , 2 types, 5 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
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 369 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
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: 1.8→47.39 Å / Num. obs: 35262 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.025 Å2 / CC1/2: 0.903 / Rmerge(I) obs: 0.288 / Net I/σ(I): 3.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5132 / CC1/2: 0.452 / % 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: 1.8→45.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23497 1672 4.8 %RANDOM
Rwork0.21037 ---
obs0.21156 33419 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å21.05 Å2
2---0.81 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 77 361 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132805
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172404
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.643856
X-RAY DIFFRACTIONr_angle_other_deg2.3881.5895556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7465347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4522.536138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.0931514
X-RAY DIFFRACTIONr_chiral_restr0.0420.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023189
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02621
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_it0.3851.5711385
X-RAY DIFFRACTIONr_mcbond_other0.3831.5651378
X-RAY DIFFRACTIONr_mcangle_it0.6522.3471723
X-RAY DIFFRACTIONr_mcangle_other0.6522.3481724
X-RAY DIFFRACTIONr_scbond_it0.3691.6291420
X-RAY DIFFRACTIONr_scbond_other0.3691.6311421
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6062.4312132
X-RAY DIFFRACTIONr_long_range_B_refined3.40319.5693363
X-RAY DIFFRACTIONr_long_range_B_other3.05218.9073276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 119 -
Rwork0.271 2473 -
obs--98.78 %

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