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- PDB-6l4n: Domain swapped dimer of Monellin loop1 mutant with QVPAG motif -

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Basic information

Entry
Database: PDB / ID: 6l4n
TitleDomain swapped dimer of Monellin loop1 mutant with QVPAG motif
ComponentsSingle chain Monellin
KeywordsPLANT PROTEIN / Monomer / L1 mutant
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.431 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: Domain swapped dimer of Monellin lopp1 mutant with QVPAG motif
Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S.
History
DepositionOct 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,1896
Polymers21,0922
Non-polymers974
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-57 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.960, 47.960, 85.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 27 or resid 29 through 30 or resid 32 through 90))
21(chain B and (resid 1 through 30 or resid 32 through 90))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 27 or resid 29 through 30 or resid 32 through 90))A1 - 27
121(chain A and (resid 1 through 27 or resid 29 through 30 or resid 32 through 90))A29 - 30
131(chain A and (resid 1 through 27 or resid 29 through 30 or resid 32 through 90))A32 - 90
211(chain B and (resid 1 through 30 or resid 32 through 90))B1 - 30
221(chain B and (resid 1 through 30 or resid 32 through 90))B32 - 90

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Components

#1: Protein Single chain Monellin


Mass: 10546.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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. Residues 48-57 YENEGFREIK have been replaced with QVPA.

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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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 20% PEG 3350, 200mM Sodium thiocyanate 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.43→41.872 Å / Num. obs: 7283 / % possible obs: 93.4 % / Redundancy: 2.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.037 / Rrim(I) all: 0.062 / Net I/σ(I): 11.1
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
2.43-2.522.30.22717477550.8460.1740.2883.394.1
9.09-41.872.70.0273851440.9970.020.03421.585.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9A

2o9a


Resolution: 2.431→41.87 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.43
RfactorNum. reflection% reflectionSelection details
Rfree0.253 386 5.31 %RANDOM
Rwork0.1963 ---
obs0.1994 7265 92.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.24 Å2 / Biso mean: 35.5651 Å2 / Biso min: 16.48 Å2
Refinement stepCycle: final / Resolution: 2.431→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 4 55 1520
Biso mean--33.31 34.66 -
Num. residues----179
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A520X-RAY DIFFRACTION9.529TORSIONAL
12B520X-RAY DIFFRACTION9.529TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.431-2.78240.36751220.2779217791
2.7824-3.50520.28421330.215236296
3.5052-41.870.20111310.1626234091

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