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- PDB-7eua: X-ray structure of a P93A Monellin mutant -

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Basic information

Entry
Database: PDB / ID: 7eua
TitleX-ray structure of a P93A Monellin mutant
ComponentsMonellin
KeywordsPLANT PROTEIN / W4Y / F19W / P93A / X-ray crystal structure
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsManjula, R. / Bhatia, S. / Jayant, B. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: X-ray structure of a P93A Monellin mutant
Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S.
History
DepositionMay 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6013
Polymers11,4091
Non-polymers1922
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.741, 64.940, 26.741
Angle α, β, γ (deg.)90.000, 109.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Monellin


Mass: 11409.012 Da / Num. of mol.: 1 / Mutation: W4Y, F19W, P93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe complete sequence of single chain Monellin has been deposited to NCBI with accession code ...The complete sequence of single chain Monellin has been deposited to NCBI with accession code AFF58925. W4Y, F19W, P93A represent mutations.

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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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→64.94 Å / Num. obs: 3068 / % possible obs: 93.9 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 14.3 / Num. measured all: 18402 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.43-2.525.60.21217143040.9670.0960.233694.7
9.09-64.9460.05384640.9990.0220.05522.494.8

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Processing

Software
NameVersionClassification
PHENIX1.82refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9U

2o9u


Resolution: 2.43→32.47 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 153 5.01 %
Rwork0.205 2898 -
obs0.2072 3051 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.74 Å2 / Biso mean: 29.0322 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 2.43→32.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 10 12 766
Biso mean--50.57 32.68 -
Num. residues----91

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