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- PDB-6rgu: Photorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-... -

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Basic information

Entry
Database: PDB / ID: 6rgu
TitlePhotorhabdus asymbiotica lectin PHL in complex with 3-O-methyl-D-glucose
ComponentsLectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / 3-O-methyl-d-glucose / 3OMG / beta-propeller
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / 3-O-methyl-beta-D-glucopyranose / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
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 1.3Jan 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)42,01317
Polymers40,2131
Non-polymers1,80016
Water5,080282
1
A: Lectin PHL
hetero molecules

A: Lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,02634
Polymers80,4262
Non-polymers3,59932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area10070 Å2
ΔGint-111 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.828, 80.828, 113.243
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-416-

NA

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Components

#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
#2: 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGlcp[3Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
3-methyl-b-D-glucopyranoseCOMMON NAMEGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.72 %
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→44.02 Å / Num. obs: 43779 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 26.515 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6310 / CC1/2: 0.693 / % 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→40.45 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.386 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2206 5 %RANDOM
Rwork0.16871 ---
obs0.17015 41534 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 112 282 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182491
X-RAY DIFFRACTIONr_angle_refined_deg1.41.6654004
X-RAY DIFFRACTIONr_angle_other_deg1.331.625777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81822.254142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15515388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0721516
X-RAY DIFFRACTIONr_chiral_restr0.0590.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
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_it1.4352.7791397
X-RAY DIFFRACTIONr_mcbond_other1.4342.7781396
X-RAY DIFFRACTIONr_mcangle_it2.0464.1631749
X-RAY DIFFRACTIONr_mcangle_other2.0454.1641750
X-RAY DIFFRACTIONr_scbond_it1.8142.9741502
X-RAY DIFFRACTIONr_scbond_other1.8142.9751503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6564.4122246
X-RAY DIFFRACTIONr_long_range_B_refined3.89833.4053415
X-RAY DIFFRACTIONr_long_range_B_other3.75333.0713366
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
Rfree0.314 167 -
Rwork0.273 3026 -
obs--99.97 %

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