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- PDB-5z1p: Structural basis of the improved sweetness and stability of the s... -

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Basic information

Entry
Database: PDB / ID: 5z1p
TitleStructural basis of the improved sweetness and stability of the single-chain sweet-tasting protein monellin (MNEI)
ComponentsMonellin chain B,Monellin chain A
KeywordsPLANT PROTEIN / monellin
Function / homologyMonellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B
Function and homology information
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLiu, B.
CitationJournal: Biochimie / Year: 2018
Title: Structure basis of the improved sweetness and thermostability of a unique double-sites single-chain sweet-tasting protein monellin (MNEI) mutant
Authors: Zhao, M. / Xu, X. / Liu, B.
History
DepositionDec 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
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: Monellin chain B,Monellin chain A
B: Monellin chain B,Monellin chain A
C: Monellin chain B,Monellin chain A
D: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)45,3844
Polymers45,3844
Non-polymers00
Water4,990277
1
A: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3461
Polymers11,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3461
Polymers11,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3461
Polymers11,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Monellin chain B,Monellin chain A


Theoretical massNumber of molelcules
Total (without water)11,3461
Polymers11,3461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.603, 46.126, 70.176
Angle α, β, γ (deg.)71.22, 79.00, 67.32
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11346.002 Da / Num. of mol.: 4 / Mutation: E2N, E23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Sodium Aceteta, 0.1M Tris PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29868 / % possible obs: 96.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.081 / Rsym value: 0.152 / Net I/σ(I): 12.75
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.418 / Num. unique obs: 1400 / Rpim(I) all: 0.252 / Rsym value: 0.452 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7


Resolution: 1.89→40.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.503 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26577 1502 5 %RANDOM
Rwork0.21551 ---
obs0.21808 28361 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.01 Å2
2---0.05 Å2-0.09 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.89→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 0 277 3315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023134
X-RAY DIFFRACTIONr_bond_other_d0.0020.023020
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9764219
X-RAY DIFFRACTIONr_angle_other_deg0.84236948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.485361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85123.145159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9211528
X-RAY DIFFRACTIONr_chiral_restr0.1060.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it2.7143.0031465
X-RAY DIFFRACTIONr_mcbond_other2.7153.0031464
X-RAY DIFFRACTIONr_mcangle_it3.6944.4811819
X-RAY DIFFRACTIONr_mcangle_other3.6934.4821820
X-RAY DIFFRACTIONr_scbond_it3.3993.4271669
X-RAY DIFFRACTIONr_scbond_other3.3993.4271669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9624.9892400
X-RAY DIFFRACTIONr_long_range_B_refined6.56625.4623683
X-RAY DIFFRACTIONr_long_range_B_other6.50525.1123592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.891→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 102 -
Rwork0.279 1778 -
obs--81.56 %

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