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- PDB-7b7e: Room temperature X-ray structure of perdeuterated PLL lectin -

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Basic information

Entry
Database: PDB / ID: 7b7e
TitleRoom temperature X-ray structure of perdeuterated PLL lectin
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / Uncharacterized protein
Function and homology information
Biological speciesPhotorhabdus laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 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 9, 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: PLL lectin


Theoretical massNumber of molelcules
Total (without water)41,9451
Polymers41,9451
Non-polymers00
Water7,062392
1
A: PLL lectin

A: PLL lectin

A: PLL lectin

A: PLL lectin


Theoretical massNumber of molelcules
Total (without water)167,7804
Polymers167,7804
Non-polymers00
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 area7490 Å2
ΔGint-35 kcal/mol
Surface area46210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.630, 89.280, 159.220
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-534-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 sodium acetate, pD 4.2, 6% (w/v) PEG 4000 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: 1.6→46 Å / Num. obs: 68418 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.3
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 5004 / CC1/2: 0.7

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Processing

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

5c9o


Resolution: 1.6→30.91 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.8624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1702 3419 5 %
Rwork0.1496 64994 -
obs0.1506 68413 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 0 392 3142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513114
X-RAY DIFFRACTIONf_angle_d0.83244322
X-RAY DIFFRACTIONf_chiral_restr0.0616482
X-RAY DIFFRACTIONf_plane_restr0.0046562
X-RAY DIFFRACTIONf_dihedral_angle_d2.94922821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.6011400.55342668X-RAY DIFFRACTION99.93
1.62-1.650.43831410.44372680X-RAY DIFFRACTION99.96
1.65-1.670.40731390.36192664X-RAY DIFFRACTION99.89
1.67-1.70.28791420.29032682X-RAY DIFFRACTION100
1.7-1.730.27711420.23912706X-RAY DIFFRACTION99.96
1.73-1.760.20031400.20262654X-RAY DIFFRACTION99.96
1.76-1.790.20841420.18232711X-RAY DIFFRACTION100
1.79-1.830.19491410.17792667X-RAY DIFFRACTION99.96
1.83-1.870.21811410.16892682X-RAY DIFFRACTION100
1.87-1.910.19421430.16972711X-RAY DIFFRACTION99.93
1.91-1.960.18911410.16522689X-RAY DIFFRACTION100
1.96-2.020.17151420.16772699X-RAY DIFFRACTION100
2.02-2.080.16861410.16512678X-RAY DIFFRACTION99.96
2.08-2.140.18031420.16092704X-RAY DIFFRACTION99.93
2.14-2.220.17871430.15222708X-RAY DIFFRACTION99.93
2.22-2.310.16061410.14322684X-RAY DIFFRACTION99.96
2.31-2.410.15871430.15822720X-RAY DIFFRACTION99.97
2.41-2.540.15271430.15282713X-RAY DIFFRACTION99.93
2.54-2.70.18361430.15582711X-RAY DIFFRACTION99.93
2.7-2.910.18261440.15432730X-RAY DIFFRACTION99.93
2.91-3.20.17961430.13452726X-RAY DIFFRACTION99.86
3.2-3.660.13841450.12382755X-RAY DIFFRACTION99.9
3.66-4.610.12141460.0962779X-RAY DIFFRACTION100
4.61-30.910.12341510.11072873X-RAY DIFFRACTION99.18

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