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- PDB-5o7k: Crystal structure of a single chain monellin mutant (Y65R) pH 2.0 -

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Basic information

Entry
Database: PDB / ID: 5o7k
TitleCrystal structure of a single chain monellin mutant (Y65R) pH 2.0
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / SWEET PROTEIN / SWEETENER
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPica, A. / Merlino, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italy
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: pH driven fibrillar aggregation of the super-sweet protein Y65R-MNEI: A step-by-step structural analysis.
Authors: Pica, A. / Leone, S. / Di Girolamo, R. / Donnarumma, F. / Emendato, A. / Rega, M.F. / Merlino, A. / Picone, D.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 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

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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)22,9486
Polymers22,5642
Non-polymers3844
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Equilibrium between monomer and dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-51 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.912, 31.501, 45.743
Angle α, β, γ (deg.)90.00, 106.24, 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: 11281.872 Da / Num. of mol.: 2 / Mutation: Y65R,Y65R
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.: 134 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2 / Details: 33% PEG4000, 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 11277 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.55
Reflection shellResolution: 2.05→2.18 Å / Rmerge(I) obs: 0.674 / Num. unique obs: 1769 / CC1/2: 0.847 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9U

2o9u


Resolution: 2.05→61.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.139 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25241 626 5.6 %RANDOM
Rwork0.19299 ---
obs0.19637 10651 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å2-0.15 Å2
2--1.12 Å20 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 2.05→61.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 20 134 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021624
X-RAY DIFFRACTIONr_bond_other_d0.0020.021519
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.9812189
X-RAY DIFFRACTIONr_angle_other_deg1.04233528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5675191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26823.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3515297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2891517
X-RAY DIFFRACTIONr_chiral_restr0.1210.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211770
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02359
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_it1.3841.825749
X-RAY DIFFRACTIONr_mcbond_other1.3841.824748
X-RAY DIFFRACTIONr_mcangle_it2.3162.717936
X-RAY DIFFRACTIONr_mcangle_other2.3152.718937
X-RAY DIFFRACTIONr_scbond_it1.5212.08875
X-RAY DIFFRACTIONr_scbond_other1.4892.062859
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4313.0081226
X-RAY DIFFRACTIONr_long_range_B_refined5.16721.0891776
X-RAY DIFFRACTIONr_long_range_B_other5.14120.7631755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5384 / 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: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 38 -
Rwork0.306 774 -
obs--96.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34160.2275-0.1390.97320.32650.3236-0.05390.00240.001-0.01450.0281-0.01310.0108-0.03760.02570.08360.01430.01390.18280.0010.041414.270223.772715.1921
20.7309-0.7315-0.60811.7457-0.49441.7086-0.03130.0547-0.06670.0744-0.1295-0.0253-0.00850.05840.16080.0127-0.01440.00270.2676-0.00920.01574.549620.034534.5065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 96
2X-RAY DIFFRACTION2B1 - 96

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