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- PDB-7bb4: Crystal structure of perdeuterated PLL lectin in complex with L-fucose -

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Basic information

Entry
Database: PDB / ID: 7bb4
TitleCrystal structure of perdeuterated PLL lectin in complex with L-fucose
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / Complex / propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / alpha-L-fucopyranose / beta-L-fucopyranose / Uncharacterized protein
Function and homology information
Biological speciesPhotorhabdus laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: Structure / Year: 2021
Title: Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions.
Authors: Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
History
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,92317
Polymers41,9451
Non-polymers1,97816
Water10,683593
1
A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,69268
Polymers167,7804
Non-polymers7,91264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area25800 Å2
ΔGint23 kcal/mol
Surface area44960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.839, 88.302, 158.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

21A-920-

HOH

31A-1020-

HOH

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Components

#1: Protein PLL lectin


Mass: 41944.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: CKY10_20885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A329WTS5
#2: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na/K tartrate dissolved in D2O, co-crystallized with 50 mM L-fucose dissolved in D2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.7→56 Å / Num. obs: 55209 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 2949 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c9o

5c9o


Resolution: 1.7→45.82 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1993 2785 5.05 %
Rwork0.1717 52329 -
obs0.1731 55114 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 131 593 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063118
X-RAY DIFFRACTIONf_angle_d0.87924303
X-RAY DIFFRACTIONf_chiral_restr0.0582499
X-RAY DIFFRACTIONf_plane_restr0.0046531
X-RAY DIFFRACTIONf_dihedral_angle_d3.60342797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.24141420.2082620X-RAY DIFFRACTION99.03
1.73-1.760.23821420.19632628X-RAY DIFFRACTION99.35
1.76-1.790.23171430.19372622X-RAY DIFFRACTION99.25
1.79-1.830.21351340.18882616X-RAY DIFFRACTION98.92
1.83-1.870.2671630.20772625X-RAY DIFFRACTION98.8
1.87-1.910.2751320.23552573X-RAY DIFFRACTION96.4
1.91-1.960.30891310.2952465X-RAY DIFFRACTION93.52
1.96-2.020.19661330.18542606X-RAY DIFFRACTION98.1
2.02-2.070.21611280.16792676X-RAY DIFFRACTION99.4
2.07-2.140.18431300.16782629X-RAY DIFFRACTION98.68
2.14-2.220.18951370.18692626X-RAY DIFFRACTION98.43
2.22-2.310.27841430.27682607X-RAY DIFFRACTION98.25
2.31-2.410.20731370.17742612X-RAY DIFFRACTION98.18
2.41-2.540.19691240.16642500X-RAY DIFFRACTION92.82
2.54-2.70.191400.16062679X-RAY DIFFRACTION99.3
2.7-2.910.19541510.15622650X-RAY DIFFRACTION98.94
2.91-3.20.15281580.13222636X-RAY DIFFRACTION98.87
3.2-3.660.18791100.13882565X-RAY DIFFRACTION93.17
3.66-4.610.15881440.12792696X-RAY DIFFRACTION98.24
4.61-45.820.16831630.15362698X-RAY DIFFRACTION94.92

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