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- PDB-6rg2: Photorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-g... -

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Basic information

Entry
Database: PDB / ID: 6rg2
TitlePhotorhabdus laumondii lectin PLL2 in complex with 3-O-methyl-D-glucose
Componentslectin PLL2 from Photorhabdus laumondii
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / 3-O-methyl-D-glucose / 3OMG / beta-propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / 3-O-methyl-beta-D-glucopyranose / ACETATE ION / 3-O-methyl-alpha-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: 1.12 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
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
B: lectin PLL2 from Photorhabdus laumondii
A: lectin PLL2 from Photorhabdus laumondii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,33328
Polymers80,3022
Non-polymers4,03126
Water19,0781059
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: equilibrium centrifugation, AUC - sedimentation velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint20 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.646, 56.708, 108.477
Angle α, β, γ (deg.)90.00, 95.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein lectin PLL2 from Photorhabdus laumondii


Mass: 40150.957 Da / Num. of mol.: 2
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 (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q7N8I8

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Sugars , 2 types, 19 molecules

#2: Sugar
ChemComp-ZB1 / 3-O-methyl-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 194.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H14O6
#3: Sugar
ChemComp-3MG / 3-O-methyl-beta-D-glucopyranose / 3-O-methyl-beta-D-glucose / 3-O-methyl-D-glucose / 3-O-methyl-glucose


Type: D-saccharide, beta linking / Mass: 194.182 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DGlcp[3Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
3-methyl-b-D-glucopyranoseCOMMON NAMEGMML 1.0

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Non-polymers , 3 types, 1066 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 11% 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: 1.12→44.84 Å / Num. obs: 224157 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 7.939 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.1
Reflection shellResolution: 1.12→1.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 16606 / CC1/2: 0.74 / % possible all: 98.9

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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: 1.12→44.84 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.574 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16099 11786 5 %RANDOM
Rwork0.13641 ---
obs0.13766 224157 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.321 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.78 Å2
2---0.63 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.12→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 269 1059 6596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136012
X-RAY DIFFRACTIONr_bond_other_d0.0040.0185230
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6758344
X-RAY DIFFRACTIONr_angle_other_deg1.4951.62712166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9615782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17422.339295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81515812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.221533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026751
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021316
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_it0.7931.0982865
X-RAY DIFFRACTIONr_mcbond_other0.7931.0962861
X-RAY DIFFRACTIONr_mcangle_it0.9711.6523597
X-RAY DIFFRACTIONr_mcangle_other0.9711.6523598
X-RAY DIFFRACTIONr_scbond_it1.071.2433147
X-RAY DIFFRACTIONr_scbond_other1.071.2433148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3271.8314700
X-RAY DIFFRACTIONr_long_range_B_refined2.92415.5887417
X-RAY DIFFRACTIONr_long_range_B_other2.15614.0827038
X-RAY DIFFRACTIONr_rigid_bond_restr6.166311242
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 845 -
Rwork0.256 16606 -
obs--98.89 %

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