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- PDB-6rgw: Photorhabdus asymbiotica lectin PHL in complex with O-methylated ... -

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Basic information

Entry
Database: PDB / ID: 6rgw
TitlePhotorhabdus asymbiotica lectin PHL in complex with O-methylated PGL-1-derived disaccharide
ComponentsLectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / O-methylated saccharide / PGL-1 / beta-propeller
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose / 3,6-O-dimethyl-D-glucose / 4-(2-azanylethoxy)phenol / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHouser, J. / Fujdiarova, E. / Jancarikova, G. / 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 17, 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_conn_type / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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.ptnr2_symmetry / _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 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,93513
Polymers40,2131
Non-polymers1,72212
Water4,792266
1
A: Lectin PHL
hetero molecules

A: Lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,87026
Polymers80,4262
Non-polymers3,44424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2990 Å2
ΔGint-68 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.893, 80.893, 113.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Lectin PHL


Mass: 40213.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: PAU_00698 / Plasmid: pET25-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner(DE3) / References: UniProt: C7BLE4
#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 , 6 types, 276 molecules

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


Mass: 208.209 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H16O6
#4: Chemical ChemComp-K42 / 4-(2-azanylethoxy)phenol


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4M NaCl, 100mM Hepes, pH 7.5

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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: 1.75→44.13 Å / Num. obs: 44002 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 28.891 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6338 / CC1/2: 0.723 / % possible all: 100

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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
Starting model: 5MXE

5mxe


Resolution: 1.75→40.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.505 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20972 2209 5 %RANDOM
Rwork0.18345 ---
obs0.18479 41752 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 111 266 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132873
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182503
X-RAY DIFFRACTIONr_angle_refined_deg1.271.6653943
X-RAY DIFFRACTIONr_angle_other_deg1.2621.6315772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4055349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22621.915141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97415383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.351517
X-RAY DIFFRACTIONr_chiral_restr0.050.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
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_it1.2983.0161381
X-RAY DIFFRACTIONr_mcbond_other1.2993.0151380
X-RAY DIFFRACTIONr_mcangle_it1.9634.521726
X-RAY DIFFRACTIONr_mcangle_other1.9624.5211727
X-RAY DIFFRACTIONr_scbond_it1.5163.2551491
X-RAY DIFFRACTIONr_scbond_other1.5163.2561492
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2074.8242215
X-RAY DIFFRACTIONr_long_range_B_refined3.63536.0193335
X-RAY DIFFRACTIONr_long_range_B_other3.47535.6433281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 155 -
Rwork0.294 3050 -
obs--100 %

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