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- PDB-8jz0: Crystal structure of a single-chain monellin mutant C41A -

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Basic information

Entry
Database: PDB / ID: 8jz0
TitleCrystal structure of a single-chain monellin mutant C41A
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: 1.229 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
A: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)22,3912
Polymers22,3912
Non-polymers00
Water3,351186
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,1961
Polymers11,1961
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)11,1961
Polymers11,1961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.695, 39.748, 44.410
Angle α, β, γ (deg.)106.22, 109.25, 103.35
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11195.691 Da / Num. of mol.: 2 / Mutation: C41A
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 / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 5.0, and 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 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.229→50 Å / Num. obs: 84210 / % possible obs: 78.5 % / Redundancy: 1.785 % / CC1/2: 0.995 / Net I/σ(I): 11.02
Reflection shellResolution: 1.23→1.3 Å / Num. unique obs: 5776 / CC1/2: 0.858

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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: 1.229→35.66 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 4263 5.06 %
Rwork0.2126 --
obs0.214 84196 78.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.229→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 186 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061541
X-RAY DIFFRACTIONf_angle_d0.9172077
X-RAY DIFFRACTIONf_dihedral_angle_d10.817599
X-RAY DIFFRACTIONf_chiral_restr0.039211
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.229-1.24290.3806440.3311833X-RAY DIFFRACTION25
1.2429-1.25750.3798470.3352936X-RAY DIFFRACTION28
1.2575-1.27290.3488650.31821148X-RAY DIFFRACTION34
1.2729-1.2890.3566740.31631306X-RAY DIFFRACTION40
1.289-1.3060.3669650.30991543X-RAY DIFFRACTION44
1.306-1.32390.31431100.29871741X-RAY DIFFRACTION52
1.3239-1.34280.3478990.28692098X-RAY DIFFRACTION62
1.3428-1.36280.31091510.28832705X-RAY DIFFRACTION80
1.3628-1.38410.32761720.2892866X-RAY DIFFRACTION86
1.3841-1.40680.29051470.29532995X-RAY DIFFRACTION88
1.4068-1.43110.28581750.2833007X-RAY DIFFRACTION90
1.4311-1.45710.34511380.28253079X-RAY DIFFRACTION90
1.4571-1.48510.33251610.28273081X-RAY DIFFRACTION91
1.4851-1.51540.33541730.2633054X-RAY DIFFRACTION90
1.5154-1.54840.29951850.24933039X-RAY DIFFRACTION91
1.5484-1.58440.30291940.24533112X-RAY DIFFRACTION91
1.5844-1.6240.31561370.26233053X-RAY DIFFRACTION91
1.624-1.66790.26921700.23773154X-RAY DIFFRACTION92
1.6679-1.7170.25781450.23483114X-RAY DIFFRACTION92
1.717-1.77240.25081490.24113132X-RAY DIFFRACTION92
1.7724-1.83580.30431510.2423083X-RAY DIFFRACTION91
1.8358-1.90930.23561570.22483123X-RAY DIFFRACTION92
1.9093-1.99610.24731630.2163155X-RAY DIFFRACTION92
1.9961-2.10140.23931530.21123143X-RAY DIFFRACTION92
2.1014-2.2330.21671730.19623145X-RAY DIFFRACTION93
2.233-2.40540.25041750.19933080X-RAY DIFFRACTION92
2.4054-2.64740.22581620.20313186X-RAY DIFFRACTION93
2.6474-3.03030.23282190.19373096X-RAY DIFFRACTION94
3.0303-3.81720.19331550.17783109X-RAY DIFFRACTION92
3.8172-35.660.19211540.18632817X-RAY DIFFRACTION83

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