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- PDB-8q0r: X-ray structure of MNEI mutant Mut9 (E23A, C41A, Y65R, S76Y) -

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Basic information

Entry
Database: PDB / ID: 8q0r
TitleX-ray structure of MNEI mutant Mut9 (E23A, C41A, Y65R, S76Y)
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / rotein aggregation / functional amyloids / MNEI / Mut9 / structural analysis / protein fibrils
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily
Similarity search - Domain/homology
ACETATE ION / Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFerraro, G. / Merlino, A. / Lucignano, R. / Picone, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural insights and aggregation propensity of a super-stable monellin mutant: A new potential building block for protein-based nanostructured materials.
Authors: Lucignano, R. / Spadaccini, R. / Merlino, A. / Ami, D. / Natalello, A. / Ferraro, G. / Picone, D.
History
DepositionJul 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,8466
Polymers22,5362
Non-polymers3104
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-37 kcal/mol
Surface area10760 Å2
Unit cell
Length a, b, c (Å)134.120, 31.290, 46.100
Angle α, β, γ (deg.)90.000, 108.648, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 11267.867 Da / Num. of mol.: 2
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30-33% PEG4K, 0.1 M sodium acetate buffer pH 4.5 and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.5→35.58 Å / Num. obs: 27470 / % possible obs: 94.7 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 16.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1225 / CC1/2: 0.69 / Rpim(I) all: 0.36 / Rrim(I) all: 0.612 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→35.58 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.434 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2747 1213 4.616 %
Rwork0.2208 25065 -
all0.223 --
obs-26278 98.32 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.081 Å2-0 Å20.141 Å2
2---0.33 Å20 Å2
3---0.126 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 18 200 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171647
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.672362
X-RAY DIFFRACTIONr_angle_other_deg1.311.5923822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4520.826109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5731518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021995
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
X-RAY DIFFRACTIONr_nbd_refined0.2020.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21477
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2768
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.221
X-RAY DIFFRACTIONr_nbd_other0.1880.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.270.223
X-RAY DIFFRACTIONr_mcbond_it2.4182.378817
X-RAY DIFFRACTIONr_mcbond_other2.4182.374815
X-RAY DIFFRACTIONr_mcangle_it3.8023.5411031
X-RAY DIFFRACTIONr_mcangle_other3.8023.5431032
X-RAY DIFFRACTIONr_scbond_it2.8822.839932
X-RAY DIFFRACTIONr_scbond_other2.8642.84925
X-RAY DIFFRACTIONr_scangle_it4.4444.1131331
X-RAY DIFFRACTIONr_scangle_other4.4524.1091320
X-RAY DIFFRACTIONr_lrange_it7.99129.4111972
X-RAY DIFFRACTIONr_lrange_other7.91528.9091930
X-RAY DIFFRACTIONr_ncsr_local_group_10.160.052899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.342780.31541X-RAY DIFFRACTION82.6442
1.59-1.6340.328780.2821777X-RAY DIFFRACTION97.8892
1.634-1.6810.336900.2751769X-RAY DIFFRACTION100
1.681-1.7330.276880.2571687X-RAY DIFFRACTION98.8307
1.733-1.790.307870.251642X-RAY DIFFRACTION100
1.79-1.8520.262830.2281637X-RAY DIFFRACTION99.9419
1.852-1.9220.266740.2251564X-RAY DIFFRACTION99.8781
1.922-2.0010.249630.2081507X-RAY DIFFRACTION99.8728
2.001-2.090.24750.2131436X-RAY DIFFRACTION99.736
2.09-2.1910.305630.2071361X-RAY DIFFRACTION100
2.191-2.310.231500.2131337X-RAY DIFFRACTION99.928
2.31-2.450.228570.2051240X-RAY DIFFRACTION99.923
2.45-2.6190.316720.221173X-RAY DIFFRACTION99.7596
2.619-2.8280.288570.2171089X-RAY DIFFRACTION99.8258
2.828-3.0970.258500.2231010X-RAY DIFFRACTION99.8117
3.097-3.4620.303380.216924X-RAY DIFFRACTION99.2776
3.462-3.9950.263330.204810X-RAY DIFFRACTION99.2933
3.995-4.8880.191270.191699X-RAY DIFFRACTION99.316
4.888-6.8930.351340.254543X-RAY DIFFRACTION99.3115
6.893-100.282160.23314X-RAY DIFFRACTION97.9229

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