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- PDB-9hkg: X-ray structure of Perm2, a circularly permuted mutant of the swe... -

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Basic information

Entry
Database: PDB / ID: 9hkg
TitleX-ray structure of Perm2, a circularly permuted mutant of the sweet protein MNEI
ComponentsMonellin chain A,Monellin chain B
KeywordsPLANT PROTEIN / sweet protein
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily
Similarity search - Domain/homology
ACETIC ACID / Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsBologna, A. / Wang, P.-H. / 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
DepositionDec 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _pdbx_struct_assembly.details ..._citation.journal_volume / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,7403
Polymers11,6201
Non-polymers1202
Water1,53185
1
A: Monellin chain A,Monellin chain B
hetero molecules

A: Monellin chain A,Monellin chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4816
Polymers23,2402
Non-polymers2404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6460 Å2
ΔGint-43 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.464, 32.518, 40.824
Angle α, β, γ (deg.)90.000, 97.840, 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-312-

HOH

21A-313-

HOH

31A-363-

HOH

41A-385-

HOH

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Components

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


Mass: 11620.231 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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Precipitant: 19% (w/v) PEG 4000, 19% (v/v) 2-Propanol Buffer: 0.095 M Trisodium citrate (pH 5.5) Additive: 5% (v/v) Glycerol

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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: 1.26→39.1 Å / Num. obs: 23712 / % possible obs: 85.59 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.06587 / Rpim(I) all: 0.02871 / Rrim(I) all: 0.07209 / Net I/σ(I): 14.46
Reflection shellResolution: 1.264→1.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8873 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 1035 / CC1/2: 0.68 / CC star: 0.9 / Rpim(I) all: 0.4936 / % possible all: 37.35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→39.1 Å / SU ML: 0.1755 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 36.2494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 457 1.93 %
Rwork0.1591 23253 -
obs0.1598 23710 85.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.56 Å2
Refinement stepCycle: LAST / Resolution: 1.26→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 8 85 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0109835
X-RAY DIFFRACTIONf_angle_d0.89321121
X-RAY DIFFRACTIONf_chiral_restr0.0741110
X-RAY DIFFRACTIONf_plane_restr0.017148
X-RAY DIFFRACTIONf_dihedral_angle_d5.6363113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.450.28091140.21525612X-RAY DIFFRACTION62.51
1.45-1.820.2461650.2218732X-RAY DIFFRACTION96.7
1.82-39.10.17931780.14588909X-RAY DIFFRACTION97.3

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