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- PDB-8cf7: Dimethylated RSL-R5 in complex with cucurbit[7]uril, C121 sheet a... -

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Basic information

Entry
Database: PDB / ID: 8cf7
TitleDimethylated RSL-R5 in complex with cucurbit[7]uril, C121 sheet assembly
ComponentsRSL-R5
KeywordsSUGAR BINDING PROTEIN / lectin / cucurbituril / biomaterials / supramolecular
Function / homologycucurbit[7]uril
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsRamberg, K. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Irelandand 12/RC/2275_P2 Ireland
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Cage versus sheet: Probing the Determinants of Protein - Cucurbit[7]uril Crystalline Architectures.
Authors: Ramberg, K.O. / Crowley, P.B.
History
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RSL-R5
B: RSL-R5
C: RSL-R5
D: RSL-R5
E: RSL-R5
F: RSL-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,47329
Polymers59,0686
Non-polymers8,40523
Water16,736929
1
A: RSL-R5
B: RSL-R5
C: RSL-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,69114
Polymers29,5343
Non-polymers4,15711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-22 kcal/mol
Surface area13170 Å2
MethodPISA
2
D: RSL-R5
E: RSL-R5
F: RSL-R5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,78315
Polymers29,5343
Non-polymers4,24912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-23 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.695, 50.396, 140.219
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein
RSL-R5


Mass: 9844.689 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 929 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 54 % / Description: hexagonal plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 25 % PEG3350 0.1 M Bis-Tris pH 5.5 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.14→46.74 Å / Num. obs: 212450 / % possible obs: 95.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 18.2
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 33.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7323 / CC1/2: 0.93 / Rpim(I) all: 0.256 / Rrim(I) all: 0.465 / % possible all: 66.3

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Processing

Software
NameVersionClassification
PHENIXv1.17refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→46.74 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 10549 4.97 %
Rwork0.1772 --
obs0.1778 212341 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 596 929 5665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055155
X-RAY DIFFRACTIONf_angle_d0.8997311
X-RAY DIFFRACTIONf_dihedral_angle_d9.4731260
X-RAY DIFFRACTIONf_chiral_restr0.082665
X-RAY DIFFRACTIONf_plane_restr0.0161111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.25232090.23954570X-RAY DIFFRACTION64
1.15-1.170.25682930.23625032X-RAY DIFFRACTION72
1.17-1.180.24272850.22135611X-RAY DIFFRACTION79
1.18-1.190.18833250.21755950X-RAY DIFFRACTION85
1.19-1.210.20552950.21056369X-RAY DIFFRACTION90
1.21-1.230.21553360.20946474X-RAY DIFFRACTION92
1.23-1.240.23382970.20096602X-RAY DIFFRACTION93
1.24-1.260.23623980.19576753X-RAY DIFFRACTION95
1.26-1.280.20523460.20056733X-RAY DIFFRACTION96
1.28-1.30.20244070.19456807X-RAY DIFFRACTION98
1.3-1.330.1873730.19387022X-RAY DIFFRACTION99
1.33-1.350.18643240.1886919X-RAY DIFFRACTION99
1.35-1.380.18133450.19096999X-RAY DIFFRACTION99
1.38-1.40.19973260.19087103X-RAY DIFFRACTION99
1.4-1.430.19253570.18936946X-RAY DIFFRACTION99
1.43-1.470.18923750.18086906X-RAY DIFFRACTION99
1.47-1.510.17483620.18127073X-RAY DIFFRACTION99
1.51-1.550.2043570.17766992X-RAY DIFFRACTION99
1.55-1.590.19173720.17767046X-RAY DIFFRACTION99
1.59-1.640.18213920.17387015X-RAY DIFFRACTION100
1.64-1.70.20633850.17397007X-RAY DIFFRACTION100
1.7-1.770.19123250.18187095X-RAY DIFFRACTION100
1.77-1.850.19153910.18117070X-RAY DIFFRACTION100
1.85-1.950.18563060.16367229X-RAY DIFFRACTION100
1.95-2.070.18693190.16727063X-RAY DIFFRACTION100
2.07-2.230.19254420.17557041X-RAY DIFFRACTION100
2.23-2.450.19263910.18127045X-RAY DIFFRACTION100
2.45-2.810.19324330.18127123X-RAY DIFFRACTION99
2.81-3.540.17913960.16717052X-RAY DIFFRACTION100
3.54-46.740.15633870.16067145X-RAY DIFFRACTION97

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