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- PDB-1lr2: Crystal structure of thaumatin at high hydrostatic pressure -

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Basic information

Entry
Database: PDB / ID: 1lr2
TitleCrystal structure of thaumatin at high hydrostatic pressure
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Taste-modifying protein / sweet protein
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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: 1.8 Å
AuthorsCharron, C. / Kadri, A. / Robert, M.C. / Capelle, B. / Giege, R. / Lorber, B.
CitationJournal: J.CRYST.GROWTH / Year: 2002
Title: X-ray diffraction properties of protein crystals prepared in agarose gel under hydrostatic pressure.
Authors: Charron, C. / Robert, M.-C. / Capelle, B. / Kadri, A. / Jenner, G. / Giege, R. / Lorber, B.
History
DepositionMay 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 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

Downloads & links

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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
Water5,062281
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

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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


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


Mass: 18.015 Da / Num. of mol.: 281 / 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: small tubes / pH: 6.5 / Details: tartrate, pH 6.5, SMALL TUBES, temperature 293.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
135 mg/mlprotein111
20.73 MNa tartrate11
30.1 MNa ADA11

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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: Apr 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 24460 / Num. obs: 24460 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.044
Reflection shellResolution: 1.8→1.85 Å / Num. unique all: 1947 / Rsym value: 0.056 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THW

1thw


Resolution: 1.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2463 -RANDOM
Rwork0.173 ---
all-24460 --
obs-24460 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 281 1841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.488
X-RAY DIFFRACTIONc_bond_d0.0073
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.197 191 -
Rwork0.166 --
obs-1756 100 %

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