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- PDB-8zxj: Sweet protein MNEI-Mut 6-1 -

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Basic information

Entry
Database: PDB / ID: 8zxj
TitleSweet protein MNEI-Mut 6-1
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / a kind of food 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: 1.5 Å
AuthorsYou, T.J. / Liu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Structural Basis for the Exceptional Thermal Stability of the Boiling-Resistant Sweet Protein MNEI.
Authors: You, T. / Shi, S. / Chen, C. / Li, J. / Xu, J. / Ma, M. / Zhu, P. / Qi, T. / Dong, T. / Wang, Y. / Ye, S. / Liu, S.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)22,6542
Polymers22,6542
Non-polymers00
Water5,477304
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3271
Polymers11,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3271
Polymers11,3271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.251, 49.737, 65.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 11326.864 Da / Num. of mol.: 2 / Mutation: I5E,E23A,I26R,Y65I,G83E,N90E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.94138 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94138 Å / Relative weight: 1
ReflectionResolution: 1.5→25.15 Å / Num. obs: 33438 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 12.9 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 33311 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.19_4092model building
PHENIX1.19_4092refinement
HKL-3000data reduction
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7


Resolution: 1.5→25.15 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1668 4.99 %
Rwork0.1915 31770 -
obs0.1937 33438 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 304 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01911636
X-RAY DIFFRACTIONf_angle_d1.59022198
X-RAY DIFFRACTIONf_chiral_restr0.1105218
X-RAY DIFFRACTIONf_plane_restr0.0171290
X-RAY DIFFRACTIONf_dihedral_angle_d13.8843642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.24511320.15632537X-RAY DIFFRACTION96.6
1.54-1.590.2171410.15822611X-RAY DIFFRACTION99.53
1.59-1.650.22611410.162611X-RAY DIFFRACTION99.85
1.65-1.710.22781290.18112619X-RAY DIFFRACTION99.49
1.71-1.790.23081490.17592619X-RAY DIFFRACTION99.82
1.79-1.890.25771630.18662633X-RAY DIFFRACTION99.82
1.89-20.23971560.1852610X-RAY DIFFRACTION99.75
2-2.160.21221350.18162646X-RAY DIFFRACTION99.14
2.16-2.380.20951260.18932662X-RAY DIFFRACTION99.64
2.38-2.720.26661210.20212690X-RAY DIFFRACTION99.57
2.72-3.420.25521200.20282727X-RAY DIFFRACTION99.51
3.42-25.150.22781550.2062805X-RAY DIFFRACTION98.86

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