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- PDB-7b7c: Room temperature X-ray structure of perdeuterated PLL lectin in c... -

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Basic information

Entry
Database: PDB / ID: 7b7c
TitleRoom temperature X-ray 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: 1.55 Å
AuthorsGajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
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 10, 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

Downloads & links

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Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9307
Polymers41,9451
Non-polymers9856
Water7,260403
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)171,72028
Polymers167,7804
Non-polymers3,94024
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 area14360 Å2
ΔGint27 kcal/mol
Surface area45800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.620, 89.070, 159.200
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-612-

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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/DCl, pD 8.1, 7% (w/v) PEG 8000 dissolved in D2O

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→46 Å / Num. obs: 74700 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.6
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 5479 / CC1/2: 0.86

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Processing

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

5c9o


Resolution: 1.55→39.8 Å / SU ML: 0.1851 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1621 3734 5 %
Rwork0.1446 70956 -
obs0.1455 74690 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 66 403 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523217
X-RAY DIFFRACTIONf_angle_d0.82824470
X-RAY DIFFRACTIONf_chiral_restr0.0594516
X-RAY DIFFRACTIONf_plane_restr0.0047571
X-RAY DIFFRACTIONf_dihedral_angle_d2.74653343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.43861360.37632581X-RAY DIFFRACTION99.82
1.57-1.590.32521370.30762622X-RAY DIFFRACTION100
1.59-1.610.25311390.25442626X-RAY DIFFRACTION99.93
1.61-1.640.3171370.23192607X-RAY DIFFRACTION99.85
1.64-1.660.19481370.21052609X-RAY DIFFRACTION99.93
1.66-1.690.21541380.1912608X-RAY DIFFRACTION99.93
1.69-1.710.17211370.1752614X-RAY DIFFRACTION99.93
1.71-1.740.18451370.16312604X-RAY DIFFRACTION99.93
1.74-1.770.21051390.1582633X-RAY DIFFRACTION99.96
1.77-1.810.1821370.15772603X-RAY DIFFRACTION99.96
1.81-1.850.18031370.16032612X-RAY DIFFRACTION99.89
1.85-1.890.18651390.16512631X-RAY DIFFRACTION99.78
1.89-1.930.18981370.16742609X-RAY DIFFRACTION99.82
1.93-1.980.15261380.15262630X-RAY DIFFRACTION99.86
1.98-2.030.16481390.14622623X-RAY DIFFRACTION99.93
2.03-2.090.1611380.14792634X-RAY DIFFRACTION99.82
2.09-2.160.16041380.1512620X-RAY DIFFRACTION99.57
2.16-2.240.16441380.14762618X-RAY DIFFRACTION99.64
2.24-2.320.21141370.14352614X-RAY DIFFRACTION99.64
2.32-2.430.18271400.16132649X-RAY DIFFRACTION99.68
2.43-2.560.14751380.14562619X-RAY DIFFRACTION99.53
2.56-2.720.19271390.15552646X-RAY DIFFRACTION99.39
2.72-2.930.17421380.15152626X-RAY DIFFRACTION99.21
2.93-3.220.14511400.1332654X-RAY DIFFRACTION99.08
3.22-3.690.13741400.12062656X-RAY DIFFRACTION98.83
3.69-4.650.10211410.09792678X-RAY DIFFRACTION98.64
4.65-39.80.12491430.11322730X-RAY DIFFRACTION96.41

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