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- PDB-3e3s: Structure of thaumatin with the magic triangle I3C -

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Basic information

Entry
Database: PDB / ID: 3e3s
TitleStructure of thaumatin with the magic triangle I3C
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Phasing tool / 5-amino-2 / 4 / 6-triiodoisophthalic acid / magic triangle / I3C
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
Chem-I3C / : / L(+)-TARTARIC ACID / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.73 Å
AuthorsBeck, T. / Gruene, T. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: A magic triangle for experimental phasing of macromolecules
Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M.
History
DepositionAug 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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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)25,32911
Polymers22,2281
Non-polymers3,10110
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.707, 57.707, 149.582
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: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6- ...THE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID MONOHYDRATE AUTHOR: T. BECK AND G.M. SHELDRICK

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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: 2.799295 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.05M ADA, 0.8M potassium sodium tartrate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2008 / Details: MULTI-LAYER OSMIC OPTICS
RadiationMonochromator: MULTI-LAYER OSMIC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→19.7 Å / Num. all: 27271 / Num. obs: 27271 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 47.5
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 24.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 25.5 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
XDSdata reduction
SADABSdata scaling
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.73→19.7 Å / Num. parameters: 7661 / Num. restraintsaints: 6878 / Occupancy max: 1 / Occupancy min: 0.19 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1361 5 %RANDOM
Rwork0.158 ---
all0.159 27271 --
obs0.158 27271 99.6 %-
Displacement parametersBiso max: 76.86 Å2 / Biso mean: 15.118 Å2 / Biso min: 0 Å2
Refine analyzeNum. disordered residues: 4
Refinement stepCycle: LAST / Resolution: 1.73→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 94 262 1868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.533
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0

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