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- PDB-7w8h: Sweet taste protein Brazzein mutant - D29K -

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Basic information

Entry
Database: PDB / ID: 7w8h
TitleSweet taste protein Brazzein mutant - D29K
Components(Defensin-like protein) x 2
KeywordsPLANT PROTEIN / Sweet taste protein / artficial sweetener
Function / homologyKnottin, scorpion toxin-like superfamily / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Defensin-like protein
Function and homology information
Biological speciesPentadiplandra brazzeana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50100444366 Å
AuthorsKim, T. / Yoon, T.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: To be published
Title: Sweet taste protein Brazzein mutant - D29K
Authors: Kim, T. / Yoon, T.
#2: Journal: FEBS Lett / Year: 1994
Title: Brazzein, a new high-potency thermostable sweet protein from Pentadiplandra brazzeana B.
Authors: Ming, D. / Hellekant, G.
#1: Journal: FEBS Lett / Year: 2003
Title: Critical regions for the sweetness of brazzein.
Authors: Jin, Z. / Danilova, V. / Assadi-Porter, F.M. / Aceti, D.J. / Markley, J.L. / Hellekant, G.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-like protein
B: Defensin-like protein
C: Defensin-like protein
D: Defensin-like protein
E: Defensin-like protein
F: Defensin-like protein
G: Defensin-like protein
H: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)52,1908
Polymers52,1908
Non-polymers00
Water5,585310
1
A: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5111
Polymers6,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Defensin-like protein


Theoretical massNumber of molelcules
Total (without water)6,5261
Polymers6,5261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.45, 55.45, 159.333
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein
Defensin-like protein / Brazzein


Mass: 6525.517 Da / Num. of mol.: 7 / Mutation: D29K
Source method: isolated from a genetically manipulated source
Details: Sweet tasting Protein Brazzein mutant D29K / Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56552
#2: Protein Defensin-like protein / Brazzein


Mass: 6511.425 Da / Num. of mol.: 1 / Mutation: D29K
Source method: isolated from a genetically manipulated source
Details: Sweet tasting Protein Brazzein mutant D29K / Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56552
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0-1.5M NaCl 1M Na-Acetate pH4.5 / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.501→27.32 Å / Num. obs: 87242 / % possible obs: 99.72 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.0709049292 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 17.34
Reflection shellResolution: 1.501→3.26 Å / Num. unique obs: 8676 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.094 / Rrim(I) all: 0.302

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4heq

4heq


Resolution: 1.50100444366→27.3145642247 Å / SU ML: 0.199638708669 / Cross valid method: FREE R-VALUE / σ(F): 1.96224378477 / Phase error: 29.5769340776
RfactorNum. reflection% reflection
Rfree0.267648052425 1970 2.25808670136 %
Rwork0.232074866384 85272 -
obs0.232861198713 87242 99.6698312598 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4584594636 Å2
Refinement stepCycle: LAST / Resolution: 1.50100444366→27.3145642247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 310 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006890558289233593
X-RAY DIFFRACTIONf_angle_d1.10386315054745
X-RAY DIFFRACTIONf_chiral_restr0.0475357891976463
X-RAY DIFFRACTIONf_plane_restr0.00411592145747618
X-RAY DIFFRACTIONf_dihedral_angle_d16.00879980591405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.502-1.53850.3402990352831360.3184693099146121X-RAY DIFFRACTION99.808581911
1.5385-1.58010.3034506505061420.2897567211946113X-RAY DIFFRACTION99.8722656874
1.5801-1.62660.3967333457681330.2872252916416061X-RAY DIFFRACTION99.8066387367
1.6266-1.67910.2523672562741440.2746524976176109X-RAY DIFFRACTION99.7766076273
1.6791-1.73910.305856121611440.2652419195876096X-RAY DIFFRACTION99.7920997921
1.7391-1.80870.2505416580551420.2588201819186081X-RAY DIFFRACTION99.8235482836
1.8087-1.8910.2862634938331380.2665900150196089X-RAY DIFFRACTION99.9037381678
1.891-1.99070.3312962198031460.2581801773676116X-RAY DIFFRACTION99.8405612245
1.9907-2.11540.3474437813841420.2576373018716093X-RAY DIFFRACTION99.8079077957
2.1154-2.27870.2808574797721420.2388195082286114X-RAY DIFFRACTION99.7767145136
2.2787-2.50780.297193737451400.236749183726098X-RAY DIFFRACTION99.8879103283
2.5078-2.87040.2494111583931440.2310208883456101X-RAY DIFFRACTION99.9519846351
2.8704-3.6150.2592222391241340.2115479546376106X-RAY DIFFRACTION99.9519461797
3.615-27.31450.2229945942691430.2039186342965974X-RAY DIFFRACTION97.388950804

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