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- PDB-5lc6: Crystal structure of a single chain monellin mutant: Q28K/C41S/Y6... -

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Basic information

Entry
Database: PDB / ID: 5lc6
TitleCrystal structure of a single chain monellin mutant: Q28K/C41S/Y65R-MNEI
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / SWEET PROTEIN
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPica, A. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione con il SudPDR-10 2011 Italy
CitationJournal: Sci Rep / Year: 2016
Title: Sweeter and stronger: enhancing sweetness and stability of the single chain monellin MNEI through molecular design.
Authors: Leone, S. / Pica, A. / Merlino, A. / Sannino, F. / Temussi, P.A. / Picone, D.
History
DepositionJun 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,9186
Polymers22,5342
Non-polymers3844
Water2,144119
1
A: Monellin chain B,Monellin chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6515
Polymers11,2671
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,2671
Polymers11,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.300, 30.990, 45.500
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 96 / Label seq-ID: 1 - 96

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11266.857 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02882, UniProt: P02881
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG4K, 0.1 M sodium acetate at pH 4.6 and 0.2 M ammonium sulfate
Temp details: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.065 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.065 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 18905 / % possible obs: 96.9 % / Redundancy: 3.8 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9U

2o9u


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.818 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22931 1028 5.4 %RANDOM
Rwork0.18822 ---
obs0.19055 17877 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 20 119 1646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021579
X-RAY DIFFRACTIONr_bond_other_d0.0090.021520
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9872123
X-RAY DIFFRACTIONr_angle_other_deg1.58933510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.78523.16579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59115293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6691515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211718
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02365
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2051.922730
X-RAY DIFFRACTIONr_mcbond_other2.2061.921729
X-RAY DIFFRACTIONr_mcangle_it3.0862.855907
X-RAY DIFFRACTIONr_mcangle_other3.0852.856908
X-RAY DIFFRACTIONr_scbond_it3.4842.492849
X-RAY DIFFRACTIONr_scbond_other3.4682.474833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2733.5241189
X-RAY DIFFRACTIONr_long_range_B_refined7.05419.2966411
X-RAY DIFFRACTIONr_long_range_B_other6.96119.1246331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10582 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 75 -
Rwork0.312 1204 -
obs--89.57 %

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