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- PDB-9myk: A domain-swapped structure of QEVKG mutant of Monellin -

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Basic information

Entry
Database: PDB / ID: 9myk
TitleA domain-swapped structure of QEVKG mutant of Monellin
ComponentsSingle-chain Monellin
KeywordsPLANT PROTEIN / domain-swapping / sweet protein / mutant
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: 2.87 Å
AuthorsManjula, R. / Subramanian, R. / Gosavi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A domain-swapped structure of QEVKG mutant of Monellin
Authors: Manjula, R. / Subramanian, R. / Gosavi, S.
History
DepositionJan 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-chain Monellin
B: Single-chain Monellin
C: Single-chain Monellin
D: Single-chain Monellin
E: Single-chain Monellin


Theoretical massNumber of molelcules
Total (without water)53,1815
Polymers53,1815
Non-polymers00
Water00
1
A: Single-chain Monellin
D: Single-chain Monellin


Theoretical massNumber of molelcules
Total (without water)21,2722
Polymers21,2722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-36 kcal/mol
Surface area10740 Å2
MethodPISA
2
B: Single-chain Monellin
C: Single-chain Monellin


Theoretical massNumber of molelcules
Total (without water)21,2722
Polymers21,2722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-37 kcal/mol
Surface area10750 Å2
MethodPISA
3
E: Single-chain Monellin

E: Single-chain Monellin


Theoretical massNumber of molelcules
Total (without water)21,2722
Polymers21,2722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area3030 Å2
ΔGint-24 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.480, 87.261, 88.874
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Single-chain Monellin / Monellin chain II / Monellin chain I


Mass: 10636.226 Da / Num. of mol.: 5
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
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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG 3550, 100mM HEPES 7.0, 0.1M LiSo4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→60.92 Å / Num. obs: 15261 / % possible obs: 94.9 % / Redundancy: 2.5 % / CC1/2: 0.908 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.067 / Rrim(I) all: 0.109 / Χ2: 0.77 / Net I/σ(I): 6.4 / Num. measured all: 38731
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 98.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 1.009 / Num. measured all: 5789 / Num. unique obs: 2301 / CC1/2: 0.352 / Rpim(I) all: 0.762 / Rrim(I) all: 1.271 / Χ2: 0.79 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→60.92 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3152 634 4.5 %
Rwork0.2448 --
obs0.248 14080 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→60.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 0 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013534
X-RAY DIFFRACTIONf_angle_d1.2594776
X-RAY DIFFRACTIONf_dihedral_angle_d13.271479
X-RAY DIFFRACTIONf_chiral_restr0.063499
X-RAY DIFFRACTIONf_plane_restr0.01629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.090.3471130.30992800X-RAY DIFFRACTION98
3.09-3.40.40511560.28052766X-RAY DIFFRACTION98
3.4-3.890.38581040.26152389X-RAY DIFFRACTION83
3.93-4.910.30651220.22492657X-RAY DIFFRACTION98
4.91-60.920.27181390.23172834X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -28.737 Å / Origin y: 55.3807 Å / Origin z: 7.8671 Å
111213212223313233
T0.6153 Å20.0107 Å2-0.0348 Å2-0.5257 Å20.0642 Å2--0.5468 Å2
L0.8816 °2-0.2887 °2-0.3611 °2-0.2604 °20.3025 °2---0.3103 °2
S-0.1663 Å °-0.2275 Å °-0.0346 Å °0.0089 Å °0.1267 Å °-0.0097 Å °0.055 Å °0.0636 Å °0.03 Å °
Refinement TLS groupSelection details: all

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