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- PDB-8jz1: Crystal structure of a single-chain monellin mutant C41V -

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Basic information

Entry
Database: PDB / ID: 8jz1
TitleCrystal structure of a single-chain monellin mutant C41V
ComponentsMonellin chain B,Monellin chain A
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: 1.239 Å
AuthorsYasui, N. / Ohnuma, K. / Yamashita, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H02841 Japan
Japan Society for the Promotion of Science (JSPS)21K19084 Japan
CitationJournal: Protein J. / Year: 2023
Title: Investigating the Effect of Substituting a Single Cysteine Residue on the Thermal Stability of an Engineered Sweet Protein, Single-Chain Monellin.
Authors: Ohnuma, K. / Yamashita, A. / Yasui, N.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,4472
Polymers22,4472
Non-polymers00
Water5,567309
1
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,2241
Polymers11,2241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,2241
Polymers11,2241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.115, 48.685, 47.162
Angle α, β, γ (deg.)90.00, 102.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11223.744 Da / Num. of mol.: 2 / Mutation: C41V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 6.0, 35% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.239→50 Å / Num. obs: 81703 / % possible obs: 84.6 % / Redundancy: 3.4 % / CC1/2: 0.988 / Net I/σ(I): 19.04
Reflection shellResolution: 1.24→1.3 Å / Num. unique obs: 6581 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOL

1mol


Resolution: 1.239→46 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 4027 4.93 %
Rwork0.166 --
obs0.1677 81682 84.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.239→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 0 309 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181638
X-RAY DIFFRACTIONf_angle_d1.6362212
X-RAY DIFFRACTIONf_dihedral_angle_d11.845644
X-RAY DIFFRACTIONf_chiral_restr0.083225
X-RAY DIFFRACTIONf_plane_restr0.01290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.239-1.25350.2606700.24831028X-RAY DIFFRACTION33
1.2535-1.26880.3374500.24721173X-RAY DIFFRACTION37
1.2688-1.28490.2695570.23811349X-RAY DIFFRACTION42
1.2849-1.30180.231700.2291618X-RAY DIFFRACTION50
1.3018-1.31960.2396810.21561690X-RAY DIFFRACTION54
1.3385-1.35850.23751440.22152605X-RAY DIFFRACTION82
1.3585-1.37970.28131460.20372755X-RAY DIFFRACTION88
1.3797-1.40230.22971460.19672857X-RAY DIFFRACTION91
1.4023-1.42650.22841480.19312991X-RAY DIFFRACTION93
1.4265-1.45240.27521180.18322990X-RAY DIFFRACTION94
1.4524-1.48040.25831810.18272942X-RAY DIFFRACTION94
1.5106-1.54350.22061760.17012937X-RAY DIFFRACTION95
1.5435-1.57940.18661440.16843031X-RAY DIFFRACTION95
1.5794-1.61890.19541680.17183016X-RAY DIFFRACTION95
1.6189-1.66260.18811430.16252987X-RAY DIFFRACTION96
1.6626-1.71160.21041560.16843048X-RAY DIFFRACTION96
1.7116-1.76680.20841270.16813065X-RAY DIFFRACTION95
1.7668-1.830.2141640.17213041X-RAY DIFFRACTION96
1.83-1.90320.17771920.16252962X-RAY DIFFRACTION96
1.9032-1.98980.16681510.16663085X-RAY DIFFRACTION96
1.9898-2.09470.21161450.15163030X-RAY DIFFRACTION96
2.0947-2.2260.17741870.1513027X-RAY DIFFRACTION96
2.226-2.39790.18051620.16033056X-RAY DIFFRACTION97
2.3979-2.63910.22391530.17253049X-RAY DIFFRACTION96
2.6391-3.0210.20241810.1623089X-RAY DIFFRACTION98
3.021-3.80580.16821570.14233079X-RAY DIFFRACTION98

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