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- PDB-8q0s: X-ray structure of the single chain monellin derivative MNEI -

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Basic information

Entry
Database: PDB / ID: 8q0s
TitleX-ray structure of the single chain monellin derivative MNEI
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / protein aggregation / functional amyloids / monellin / MNEI / protein fibrils
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Cystatin superfamily / ACETATE ION / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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

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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)23,1637
Polymers22,8382
Non-polymers3255
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-16 kcal/mol
Surface area11230 Å2
Unit cell
Length a, b, c (Å)31.650, 38.970, 44.130
Angle α, β, γ (deg.)105.995, 109.521, 103.361
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: 11419.049 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 / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
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: 1.19→38.39 Å / Num. obs: 52760 / % possible obs: 92.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.024 / Rrim(I) all: 0.044 / Net I/σ(I): 14.2
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.679 / Num. unique obs: 2446 / CC1/2: 0.726 / Rpim(I) all: 0.443 / Rrim(I) all: 0.815 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→38.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.146 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2562 2465 4.929 %
Rwork0.2161 47541 -
all0.218 --
obs-50006 87.278 %
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: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å2-0.027 Å20.036 Å2
2--0.036 Å2-0.023 Å2
3----0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.19→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 21 263 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131899
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151808
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6712582
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5974199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32921.858113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8821516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022263
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02473
X-RAY DIFFRACTIONr_nbd_refined0.2230.2356
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21575
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2821
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1990.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.223
X-RAY DIFFRACTIONr_nbd_other0.2480.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_mcbond_it1.5141.416896
X-RAY DIFFRACTIONr_mcbond_other1.5051.414895
X-RAY DIFFRACTIONr_mcangle_it2.2872.1091156
X-RAY DIFFRACTIONr_mcangle_other2.2872.111157
X-RAY DIFFRACTIONr_scbond_it2.191.7911003
X-RAY DIFFRACTIONr_scbond_other2.1891.7941004
X-RAY DIFFRACTIONr_scangle_it3.4032.5761426
X-RAY DIFFRACTIONr_scangle_other3.4022.581427
X-RAY DIFFRACTIONr_lrange_it5.53618.512158
X-RAY DIFFRACTIONr_lrange_other5.53518.5342159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.2210.3021260.3022337X-RAY DIFFRACTION57.641
1.221-1.2540.2971210.2972550X-RAY DIFFRACTION65.2897
1.254-1.2910.341600.292867X-RAY DIFFRACTION74.7592
1.291-1.330.3191630.2853204X-RAY DIFFRACTION87.0251
1.33-1.3740.3111690.2793272X-RAY DIFFRACTION90.9836
1.374-1.4220.3271640.2693218X-RAY DIFFRACTION92.6575
1.422-1.4760.2971680.2713134X-RAY DIFFRACTION93.3824
1.476-1.5360.2811500.2583012X-RAY DIFFRACTION93.8836
1.536-1.6040.2931640.2422907X-RAY DIFFRACTION94.0294
1.604-1.6820.2591500.2362716X-RAY DIFFRACTION91.4486
1.682-1.7730.2511540.2292659X-RAY DIFFRACTION94.8096
1.773-1.880.2351370.2162498X-RAY DIFFRACTION95.0577
1.88-2.010.231170.2062380X-RAY DIFFRACTION94.943
2.01-2.170.261110.2062179X-RAY DIFFRACTION94.2387
2.17-2.3770.2471050.1962022X-RAY DIFFRACTION93.5356
2.377-2.6560.273820.2121879X-RAY DIFFRACTION95.9393
2.656-3.0640.291760.2031607X-RAY DIFFRACTION95.1923
3.064-3.7470.218550.1751403X-RAY DIFFRACTION94.4912
3.747-5.2740.211690.1671071X-RAY DIFFRACTION97.5192
5.274-100.215230.215617X-RAY DIFFRACTION96.823

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