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- PDB-3pxm: Reduced sweetness of a monellin (MNEI) mutant results from increa... -

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Basic information

Entry
Database: PDB / ID: 3pxm
TitleReduced sweetness of a monellin (MNEI) mutant results from increased protein flexibility and disruption of a distant poly-(L-proline) II helix
ComponentsMonellin chain B/Monellin chain A chimeric protein
KeywordsPLANT PROTEIN / a poly-(L-proline) II (PPII) helix / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHobbs, J.R. / Templeton, C.M. / Pour, S.O. / Blanch, E.W. / Munger, S.M. / Conn, G.L.
CitationJournal: Chem Senses / Year: 2011
Title: Reduced Sweetness of a Monellin (MNEI) Mutant Results from Increased Protein Flexibility and Disruption of a Distant Poly-(L-Proline) II Helix.
Authors: Templeton, C.M. / Ostovar Pour, S. / Hobbs, J.R. / Blanch, E.W. / Munger, S.D. / Conn, G.L.
History
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monellin chain B/Monellin chain A chimeric protein
B: Monellin chain B/Monellin chain A chimeric protein


Theoretical massNumber of molelcules
Total (without water)22,7822
Polymers22,7822
Non-polymers00
Water3,945219
1
A: Monellin chain B/Monellin chain A chimeric protein


Theoretical massNumber of molelcules
Total (without water)11,3911
Polymers11,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monellin chain B/Monellin chain A chimeric protein


Theoretical massNumber of molelcules
Total (without water)11,3911
Polymers11,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.889, 39.652, 45.153
Angle α, β, γ (deg.)84.90, 80.25, 83.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Monellin chain B/Monellin chain A chimeric protein / Monellin chain II / Monellin chain I


Mass: 11390.995 Da / Num. of mol.: 2 / Mutation: V37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Li2SO4, 0.1M HEPES and 25% w/v PEG4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.548
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 1.8→22.43 Å / Num. obs: 17472 / Redundancy: 3.5 %

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV9

1iv9


Resolution: 1.8→24.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.73 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21892 933 5.4 %RANDOM
Rwork0.17686 ---
obs0.1792 16484 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.586 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 0 219 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9742239
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9675198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47123.48886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5061514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21135
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.51014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49121576
X-RAY DIFFRACTIONr_scbond_it2.6033757
X-RAY DIFFRACTIONr_scangle_it3.8844.5662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 65 -
Rwork0.208 1159 -
obs--88.76 %

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