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- PDB-6zum: Crystal structure of dimethylated RSL-N23H (RSL-B3) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6zum
TitleCrystal structure of dimethylated RSL-N23H (RSL-B3) in complex with cucurbit[7]uril and zinc
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / cucurbituril / molecular glue / crystal engineering / dimethyllysine / zinc / b-propeller
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / ACETATE ION / beta-D-fructopyranose / cucurbit[7]uril / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsGuagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland12/RC/2275_P2 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: Metal-Mediated Protein-Cucurbituril Crystalline Architectures
Authors: Guagnini, F. / Engilberge, S. / Flood, R.J. / Ramberg, K.O. / Crowley, P.B.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6269
Polymers9,8671
Non-polymers1,7598
Water1,00956
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,87827
Polymers29,6003
Non-polymers5,27724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7810 Å2
ΔGint-214 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.057, 51.057, 102.477
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-107-

NA

21A-108-

NA

31A-251-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

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


Mass: 9866.798 Da / Num. of mol.: 1
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 (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 62 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 0.1 M TRIS-HCl pH 7.0, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.589→34.159 Å / Num. obs: 13378 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.03 / Rrim(I) all: 0.096 / Net I/σ(I): 14.3
Reflection shellResolution: 1.589→1.617 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 646 / CC1/2: 0.775 / Rpim(I) all: 0.332 / Rrim(I) all: 0.771

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7W polyalanine

6f7w


Resolution: 1.589→34.159 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 653 4.88 %
Rwork0.1861 12725 -
obs0.187 13378 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.71 Å2 / Biso mean: 43.2139 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.589→34.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 185 56 930
Biso mean--57.28 47.62 -
Num. residues----89
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013843
X-RAY DIFFRACTIONf_angle_d0.9921199
X-RAY DIFFRACTIONf_chiral_restr0.055114
X-RAY DIFFRACTIONf_plane_restr0.016176
X-RAY DIFFRACTIONf_dihedral_angle_d8.17486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5894-1.71210.28061390.234249499
1.7121-1.88440.21791440.20242562100
1.8844-2.1570.25131210.18972549100
2.157-2.71740.24561050.21222572100
2.7174-34.1590.17671440.17122548100
Refinement TLS params.Method: refined / Origin x: 6.809 Å / Origin y: 9.9386 Å / Origin z: 0.4441 Å
111213212223313233
T0.2342 Å2-0.0336 Å20.0079 Å2-0.1659 Å2-0.024 Å2--0.3361 Å2
L6.3387 °20.2581 °2-0.5308 °2-4.112 °2-0.3238 °2--2.2641 °2
S0.149 Å °-0.0694 Å °0.9768 Å °0.1229 Å °-0.0182 Å °-0.4941 Å °-0.3195 Å °0.1104 Å °-0.1162 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 301
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allB3
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1 - 2
6X-RAY DIFFRACTION1allW1 - 71

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