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- PDB-6rgg: Photorhabdus laumondii lectin PLL2 in complex with O-methylated P... -

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Basic information

Entry
Database: PDB / ID: 6rgg
TitlePhotorhabdus laumondii lectin PLL2 in complex with O-methylated PGL-1-derived disaccharide
Componentslectin PLL2 from Photorhabdus laumondii
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / PGL-1 / O-methylated saccharide / beta-propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose / 3,6-O-dimethyl-D-glucose / 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: 2.2 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 / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 24, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
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

Downloads & links

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Assembly

Deposited unit
A: lectin PLL2 from Photorhabdus laumondii
B: lectin PLL2 from Photorhabdus laumondii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11316
Polymers80,3022
Non-polymers1,81114
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, AUC - sedimentation velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-70 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.304, 89.347, 68.401
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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) / References: UniProt: Q7N8I8
#3: Sugar ChemComp-7CV / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose / 6-deoxy-2,3-di-O-methyl-alpha-L-mannose / 6-deoxy-2,3-di-O-methyl-L-mannose / 6-deoxy-2,3-di-O-methyl-mannose


Type: L-saccharide, alpha linking / Mass: 192.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O5
IdentifierTypeProgram
LRhap[2Me,3Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-methyl-3-methyl-a-L-rhamnoopyranoseCOMMON NAMEGMML 1.0

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Non-polymers , 4 types, 28 molecules

#2: Chemical
ChemComp-K3Q / 3,6-O-dimethyl-D-glucose


Mass: 208.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16O6
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 12.5% PEG 4000, 0.1 M sodium acetate pH 4.6

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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: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→67.03 Å / Num. obs: 40910 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 46.387 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5878 / CC1/2: 0.541 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→67.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22356 2033 5 %RANDOM
Rwork0.19897 ---
obs0.20019 38568 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.054 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å2-0 Å21.76 Å2
2--0.41 Å2-0 Å2
3---1.48 Å2
Refinement stepCycle: 1 / Resolution: 2.2→67.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 117 16 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135492
X-RAY DIFFRACTIONr_bond_other_d0.0370.0184726
X-RAY DIFFRACTIONr_angle_refined_deg1.431.6417546
X-RAY DIFFRACTIONr_angle_other_deg2.4311.60310900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3135675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92622.555274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12815719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0841528
X-RAY DIFFRACTIONr_chiral_restr0.0540.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026203
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021225
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_it4.1966.5312712
X-RAY DIFFRACTIONr_mcbond_other4.1936.532711
X-RAY DIFFRACTIONr_mcangle_it5.8149.7943383
X-RAY DIFFRACTIONr_mcangle_other5.8149.7953384
X-RAY DIFFRACTIONr_scbond_it4.6846.9882780
X-RAY DIFFRACTIONr_scbond_other4.6836.9892781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.94910.3214164
X-RAY DIFFRACTIONr_long_range_B_refined8.97476.4026118
X-RAY DIFFRACTIONr_long_range_B_other8.97576.4096119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 150 -
Rwork0.386 2773 -
obs--98.09 %

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