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- PDB-7w8e: Sweet taste protein Brazzein - R43A -

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Basic information

Entry
Database: PDB / ID: 7w8e
TitleSweet taste protein Brazzein - R43A
ComponentsDefensin-like protein
KeywordsPLANT PROTEIN / Sweet taste Protein / Artficial sweetner
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: 1.34 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 - R43A
Authors: Kim, T. / Yoon, T.
#1: Journal: FEBS Lett / Year: 1994
Title: Brazzein, a new high-potency thermostable sweet protein from Pentadiplandra brazzeana B.
Authors: Ming, D. / Hellekant, G.
#2: Journal: To be published
Title: Sweet taste protein Brazzein - R43A
Authors: Kim, T. / Yoon, T.
#3: 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 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2862
Polymers8,2631
Non-polymers231
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area4450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.634, 51.634, 60.618
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-239-

HOH

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Components

#1: Protein Defensin-like protein / Brazzein


Mass: 8263.392 Da / Num. of mol.: 1 / Mutation: R43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pentadiplandra brazzeana (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56552
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.5M NaCl, 1M Na-Citrate pH4.0 / PH range: 4

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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: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.34→18.42 Å / Num. obs: 20107 / % possible obs: 94 % / Redundancy: 9.9 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Rrim(I) all: 0.119 / Net I/σ(I): 23.2
Reflection shellResolution: 1.343→1.36 Å / Num. unique obs: 20107 / Rpim(I) all: 0.055 / Rrim(I) all: 0.124

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4heq

4heq


Resolution: 1.34→18.41 Å / SU ML: 0.1131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 1048 5.22 %
Rwork0.2094 19014 -
obs0.2102 20062 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.11 Å2
Refinement stepCycle: LAST / Resolution: 1.34→18.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms449 0 1 49 499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063457
X-RAY DIFFRACTIONf_angle_d0.8807612
X-RAY DIFFRACTIONf_chiral_restr0.080661
X-RAY DIFFRACTIONf_plane_restr0.005380
X-RAY DIFFRACTIONf_dihedral_angle_d5.509961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.410.22171580.22242837X-RAY DIFFRACTION100
1.41-1.50.25451550.2072852X-RAY DIFFRACTION99.93
1.5-1.620.20961610.19552865X-RAY DIFFRACTION99.77
1.62-1.780.18261680.19142836X-RAY DIFFRACTION99.83
1.78-2.040.22531470.19532884X-RAY DIFFRACTION99.74
2.04-2.570.2031600.19152868X-RAY DIFFRACTION99.12
2.57-18.410.2807990.25541872X-RAY DIFFRACTION61.67

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