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- PDB-7e7r: Crystal structure of RSL mutant in complex with Ligand -

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Basic information

Entry
Database: PDB / ID: 7e7r
TitleCrystal structure of RSL mutant in complex with 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 / Chem-R2F / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 27, 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 / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7428
Polymers58,1832
Non-polymers4,5596
Water7,224401
1
A: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3714
Polymers29,0921
Non-polymers2,2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin protein,Fucose-binding lectin protein,Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3714
Polymers29,0921
Non-polymers2,2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.427, 81.959, 97.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 29091.568 Da / Num. of mol.: 2 / Mutation: R17A,R108A,R199A
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
#2: Chemical
ChemComp-R2F / 2-[2-[4-[[(2R,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 759.888 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H53N5O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: 20 mM Tris-HCl, 100 mM of NaCl pH 7.5, Micro centrifuge tube sequentially put with RSL solution, pure b

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.82→62.64 Å / Num. obs: 49086 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.052 / Rrim(I) all: 0.191 / Net I/σ(I): 10.8 / Num. measured all: 647333 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.82-1.92131.4359176770390.9040.4091.4932.7
5.75-62.6411.30.0541942817180.9980.0170.05725.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CSD

4csd


Resolution: 1.82→62.64 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 2402 4.93 %RANDOM
Rwork0.2499 46352 --
obs0.2516 48754 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 26.8866 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.82→62.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 330 401 4641
Biso mean--62.72 26.01 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.860.35331200.332126942814100
1.86-1.90.34651360.314726842820100
1.9-1.940.30571390.299127052844100
1.94-1.990.28331360.278726922828100
1.99-2.040.30431280.274427122840100
2.04-2.10.25981530.270427032856100
2.1-2.170.35671360.255827042840100
2.17-2.250.31251310.245427052836100
2.25-2.340.31181310.252327152846100
2.34-2.450.2441540.239826822836100
2.45-2.580.27471380.250827432881100
2.58-2.740.29711480.252227042852100
2.74-2.950.29811540.248627432897100
2.95-3.240.28181400.237227412881100
3.24-3.710.25481570.225527422899100
3.71-4.680.25691480.212427922940100
4.68-62.640.28961530.25672891304498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.99430.2690.23590.37060.23161.18360.0069-0.12690.0784-0.0162-0.04740.0358-0.0501-0.06550.0310.1242-0.00040.00220.36350.00980.1282-11.1608-13.17639.4829
22.2036-0.0218-0.24320.58630.15551.49530.01990.1583-0.0699-0.0275-0.0321-0.00910.0601-0.07980.00340.10710.0024-0.0030.2805-00.117312.089213.2965-9.62
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:501)A2 - 501
2X-RAY DIFFRACTION2(chain B and resseq 1:501)B1 - 501

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