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- PDB-1ly0: Structure of thaumatin crystallized in the presence of glycerol -

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Basic information

Entry
Database: PDB / ID: 1ly0
TitleStructure of thaumatin crystallized in the presence of glycerol
ComponentsThaumatin I
KeywordsPLANT PROTEIN / TASTE-MODIFYING PROTEIN / SWEET PROTEIN
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsCharron, C. / Kadri, A. / Robert, M.C. / Giege, R. / Lorber, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization in the presence of glycerol displaces water molecules in the structure of thaumatin.
Authors: Charron, C. / Kadri, A. / Robert, M.C. / Giege, R. / Lorber, B.
History
DepositionJun 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.867, 57.867, 149.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit is a monomer

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Components

#1: Protein Thaumatin I /


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9474 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. all: 55721 / Num. obs: 55482 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.049
Reflection shellResolution: 1.36→1.41 Å / Rsym value: 0.151 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THW

1thw


Resolution: 1.36→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.204 5631 RANDOM
Rwork0.195 --
all0.196 55482 -
obs0.196 55482 -
Refinement stepCycle: LAST / Resolution: 1.36→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 325 1885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.308
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.36→1.41 Å
RfactorNum. reflection% reflection
Rfree0.24 530 -
Rwork0.219 --
obs-5268 99.9 %

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