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- PDB-6rgj: Photorhabdus asymbiotica lectin PHL in complex with D-glucose -

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Basic information

Entry
Database: PDB / ID: 6rgj
TitlePhotorhabdus asymbiotica lectin PHL in complex with D-glucose
ComponentsLectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / Photorhabdus / glucose / beta-propeller
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / beta-D-glucopyranose / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 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 / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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)41,46019
Polymers40,2131
Non-polymers1,24718
Water6,395355
1
A: Lectin PHL
hetero molecules

A: Lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,92038
Polymers80,4262
Non-polymers2,49436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8870 Å2
ΔGint-160 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.638, 80.638, 113.437
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-663-

HOH

21A-824-

HOH

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Components

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Protein / Sugars , 2 types, 5 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 / References: UniProt: C7BLE4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 56.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.9 M NaCl, 100 mM Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.8→44.03 Å / Num. obs: 40112 / % possible obs: 99.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 10.799 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Net I/σ(I): 18.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 5670 / CC1/2: 0.895 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXE

5mxe


Resolution: 1.8→44.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.38 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 2021 5 %RANDOM
Rwork0.16982 ---
obs0.17112 38051 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 71 355 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182422
X-RAY DIFFRACTIONr_angle_refined_deg1.41.643889
X-RAY DIFFRACTIONr_angle_other_deg1.3611.5875604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5085351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52922.374139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38415379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.41515
X-RAY DIFFRACTIONr_chiral_restr0.0610.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it0.9411.5551389
X-RAY DIFFRACTIONr_mcbond_other0.9411.5551388
X-RAY DIFFRACTIONr_mcangle_it1.5282.331739
X-RAY DIFFRACTIONr_mcangle_other1.5272.331740
X-RAY DIFFRACTIONr_scbond_it1.1451.6491435
X-RAY DIFFRACTIONr_scbond_other1.1451.651436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7982.4392149
X-RAY DIFFRACTIONr_long_range_B_refined4.07919.3513442
X-RAY DIFFRACTIONr_long_range_B_other3.68418.8383356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 145 -
Rwork0.268 2658 -
obs--96.19 %

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