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- PDB-6fhy: Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C... -

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Basic information

Entry
Database: PDB / ID: 6fhy
TitlePhotorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside
ComponentsLectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / C-fucoside / 4.6. 4(S)-2-Hydroxy-1-phenylethyl 2 / 3 / 4-trideoxy-3-C-[(a-L- fucopyranosyl)methyl]-b-D-threo-hexopyranoside
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / Chem-DS8 / DI(HYDROXYETHYL)ETHER / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsHouser, J. / Jancarikova, G. / Wimmerova, M.
CitationJournal: Sci Rep / Year: 2019
Title: Fucosylated inhibitors of recently identified bangle lectin from Photorhabdus asymbiotica.
Authors: Paulikova, G. / Houser, J. / Kasakova, M. / Oroszova, B. / Bertolotti, B. / Parkan, K. / Moravcova, J. / Wimmerova, M.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin PHL
B: Lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,13817
Polymers80,4262
Non-polymers3,71215
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Analytic ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-16 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.346, 81.346, 222.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lectin PHL


Mass: 40213.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: PAU_00698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: C7BLE4

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Non-polymers , 5 types, 456 molecules

#2: Chemical
ChemComp-DS8 / (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R},6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol


Mass: 292.325 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C13H24O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.7 M NaCl, 100 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.86→44.56 Å / Num. obs: 69572 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.193 / Net I/σ(I): 12.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.383 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10443 / CC1/2: 0.576 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXE

5mxe


Resolution: 1.86→44.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.304 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21536 3505 4.8 %RANDOM
Rwork0.18095 ---
obs0.18258 69572 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.86→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 242 441 5987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195785
X-RAY DIFFRACTIONr_bond_other_d0.0060.025190
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9247970
X-RAY DIFFRACTIONr_angle_other_deg0.945311920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5725701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63923.76250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21115770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4911532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021423
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_it0.9141.9372765
X-RAY DIFFRACTIONr_mcbond_other0.9141.9372764
X-RAY DIFFRACTIONr_mcangle_it1.4622.93458
X-RAY DIFFRACTIONr_mcangle_other1.4622.93459
X-RAY DIFFRACTIONr_scbond_it1.2212.1573020
X-RAY DIFFRACTIONr_scbond_other1.2212.1573020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0293.1884506
X-RAY DIFFRACTIONr_long_range_B_refined3.56117.0376930
X-RAY DIFFRACTIONr_long_range_B_other3.3116.7466748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.857→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 254 -
Rwork0.287 5027 -
obs--99.68 %

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