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- PDB-3q2p: Reduced sweetness of a monellin (MNEI) mutant results from increa... -

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Basic information

Entry
Database: PDB / ID: 3q2p
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 / sweet protein / sweet receptor / T1R2:T1R3
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: 2.341 Å
AuthorsTempleton, C.M. / Hobbs, J.R. / Munger, S.D. / 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 20, 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: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 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 / 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
C: Monellin chain B/Monellin chain A chimeric protein
D: Monellin chain B/Monellin chain A chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6435
Polymers45,6204
Non-polymers231
Water3,639202
1
A: Monellin chain B/Monellin chain A chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4282
Polymers11,4051
Non-polymers231
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)11,4051
Polymers11,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monellin chain B/Monellin chain A chimeric protein


Theoretical massNumber of molelcules
Total (without water)11,4051
Polymers11,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monellin chain B/Monellin chain A chimeric protein


Theoretical massNumber of molelcules
Total (without water)11,4051
Polymers11,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.400, 144.100, 45.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11405.021 Da / Num. of mol.: 4 / Mutation: G16A, V37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02882, UniProt: P02881
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 200 mM NaCl, 100 mM phosphate-citrate, 20% w/v PEG8000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→40 Å / Num. all: 16980 / Num. obs: 16708 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16
Reflection shellResolution: 2.34→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2480 / % possible all: 90.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREP(CCP4)phasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O9U

2o9u


Resolution: 2.341→31.4 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 846 5.07 %Random
Rwork0.1838 ---
all0.187 16683 --
obs0.187 16683 97.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.622 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2392 Å2-0 Å2-0.3766 Å2
2---0.7972 Å20 Å2
3----0.442 Å2
Refinement stepCycle: LAST / Resolution: 2.341→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 1 202 3387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083285
X-RAY DIFFRACTIONf_angle_d1.0374427
X-RAY DIFFRACTIONf_dihedral_angle_d14.3511276
X-RAY DIFFRACTIONf_chiral_restr0.069440
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3407-2.48720.31191200.19732308X-RAY DIFFRACTION85
2.4872-2.67920.31941500.20342712X-RAY DIFFRACTION100
2.6792-2.94860.27331460.20272674X-RAY DIFFRACTION100
2.9486-3.37490.26221400.18562713X-RAY DIFFRACTION100
3.3749-4.25030.21721530.16282697X-RAY DIFFRACTION100
4.2503-31.40280.19111370.16792733X-RAY DIFFRACTION99

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