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- PDB-7e7w: Crystal structure of RSL mutant in complex with sugar Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7w
TitleCrystal structure of RSL mutant in complex with sugar Ligand
ComponentsFucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex / Lectin / Fucose / Rhodamine
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsLi, L. / Chen, G.S.
CitationJournal: ACS Nano / Year: 2023
Title: Spatiotemporal Landscape for the Sophisticated Transformation of Protein Assemblies Defined by Multiple Supramolecular Interactions.
Authors: Long Li / Zhen Li / Ziying Wang / Shuyu Chen / Rongying Liu / Xuyang Xu / Zhi Zhang / Linfei Ye / Yu Ding / Quan Luo / Sheng Cao / Lei Zhang / Anne Imberty / Guosong Chen /
Abstract: Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate ...Precise protein assemblies not only constitute a series of living machineries but also provide an advanced class of biomaterials. Previously, we developed the inducing ligand strategy to generate various fixed protein assemblies, without the formation of noncovalent interactions between proteins. Here, we demonstrated that controlling the symmetry and number of supramolecular interactions introduced on protein surfaces could direct the formation of unspecific interactions between proteins and induce various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulation of the protein's native surfaces. More importantly, these nanoscale assemblies could spontaneously evolve into more ordered architectures, crystals. We further showed that the transformation from the introduced supramolecular interactions to the interactions formed between proteins was crucial for pathway selection and outcomes of evolution. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
History
DepositionFeb 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 1.2Jul 29, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)88,0503
Polymers88,0503
Non-polymers00
Water00
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein


Theoretical massNumber of molelcules
Total (without water)29,3501
Polymers29,3501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.567, 46.554, 103.254
Angle α, β, γ (deg.)90.040, 89.920, 119.980
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 29349.916 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 20 mM Tris-HCl, 100 mM of NaCl pH 7.5, the crystal was obtained in Micro centrifuge tube sequentially put with RSL solution, pure buffer, and the ligand solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 4.1→30 Å / Num. obs: 6095 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.078 / Rrim(I) all: 0.143 / Χ2: 0.718 / Net I/σ(I): 4.7 / Num. measured all: 19061
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.1-4.2530.46290.8690.2630.480.84398.9
4.25-4.4230.2816060.9210.1860.3380.88799.2
4.42-4.623.10.1976050.970.1270.2350.9299
4.62-4.863.20.2226030.9410.140.2630.8599.2
4.86-5.1630.1256200.9850.0840.1510.7899
5.16-5.562.90.145810.9580.0950.1710.70899.7
5.56-6.113.20.146260.9630.0910.1680.65799.7
6.11-6.993.40.1076110.9850.0660.1260.63898.7
6.99-8.773.30.0635960.9930.0390.0740.45799.2
8.77-303.10.0386180.990.0250.0450.47899.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSD

4csd


Resolution: 4.1→26.2 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3467 245 4.24 %RANDOM
Rwork0.2004 5530 --
obs0.2063 5775 98.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.52 Å2 / Biso mean: 82.1568 Å2 / Biso min: 31.08 Å2
Refinement stepCycle: final / Resolution: 4.1→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 0 0 6063
Num. residues----792
LS refinement shellResolution: 4.101→4.247 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 18 -
Rwork0.1588 622 -
obs--99 %

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