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- PDB-9hik: X-ray structure of Perm3, a circularly permuted mutant of the swe... -

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Basic information

Entry
Database: PDB / ID: 9hik
TitleX-ray structure of Perm3, a circularly permuted mutant of the sweet protein MNEI
ComponentsMonellin chain A,Monellin chain B
KeywordsPLANT PROTEIN / sweet protein
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBologna, A. / Wang, P.-H. / Lucignano, R. / Essen, L.-O. / Spadaccini, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government Italy
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Unravelling the amyloid aggregation mechanism of the sweet protein Monellin: Insights from circular permutated mutants.
Authors: Lucignano, R. / Bologna, A. / Gramazio, S. / Wang, P.H. / Taxis, C. / Essen, L.O. / Picone, D. / Spadaccini, R.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monellin chain A,Monellin chain B


Theoretical massNumber of molelcules
Total (without water)11,5631
Polymers11,5631
Non-polymers00
Water2,828157
1
A: Monellin chain A,Monellin chain B

A: Monellin chain A,Monellin chain B


Theoretical massNumber of molelcules
Total (without water)23,1262
Polymers23,1262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6170 Å2
ΔGint-39 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.451, 32.446, 41.484
Angle α, β, γ (deg.)90.000, 97.580, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21A-194-

HOH

31A-209-

HOH

41A-232-

HOH

51A-251-

HOH

61A-255-

HOH

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Components

#1: Protein Monellin chain A,Monellin chain B / Monellin chain I / Monellin chain II


Mass: 11563.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli B (bacteria) / References: UniProt: P02881, UniProt: P02882
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Precipitant: 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol Buffer: 0.085 M Sodium citrate (pH 5.6) Salt: 0.17 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→30.41 Å / Num. obs: 34452 / % possible obs: 92.61 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.74 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0624 / Rpim(I) all: 0.0273 / Rrim(I) all: 0.0683 / Net I/σ(I): 15.22
Reflection shellResolution: 1.15→1.24 Å / Rmerge(I) obs: 0.5609 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 5551 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.2841 / Rrim(I) all: 0.6323 / % possible all: 75.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→30.41 Å / SU ML: 0.1276 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 27.3527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1874 644 1.87 %
Rwork0.159 33808 -
obs0.1595 34452 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.26 Å2
Refinement stepCycle: LAST / Resolution: 1.15→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 0 157 950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055846
X-RAY DIFFRACTIONf_angle_d0.72761146
X-RAY DIFFRACTIONf_chiral_restr0.0721115
X-RAY DIFFRACTIONf_plane_restr0.0104152
X-RAY DIFFRACTIONf_dihedral_angle_d12.7445340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.240.2285860.23755465X-RAY DIFFRACTION75.34
1.24-1.360.22351410.16916902X-RAY DIFFRACTION95.32
1.36-1.560.18731390.15687033X-RAY DIFFRACTION96.63
1.56-1.970.20251370.16187108X-RAY DIFFRACTION97.33
1.97-30.410.17651410.15297300X-RAY DIFFRACTION98.21

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