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- PDB-5fgx: Thaumatin solved by native sulphur SAD using synchrotron radiation -

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Basic information

Entry
Database: PDB / ID: 5fgx
TitleThaumatin solved by native sulphur SAD using synchrotron radiation
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / sulphur SAD / synchrotron
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 / SAD / Resolution: 2.134 Å
AuthorsNass, K.J. / Meinhart, A. / Barends, T.R.M. / Foucar, L. / Gorel, A. / Aquila, A. / Botha, S. / Doak, R.B. / Koglin, J. / Liang, M. ...Nass, K.J. / Meinhart, A. / Barends, T.R.M. / Foucar, L. / Gorel, A. / Aquila, A. / Botha, S. / Doak, R.B. / Koglin, J. / Liang, M. / Shoeman, R.L. / Williams, G.J. / Boutet, S. / Schlichting, I.
CitationJournal: Iucrj / Year: 2016
Title: Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data.
Authors: Nass, K. / Meinhart, A. / Barends, T.R. / Foucar, L. / Gorel, A. / Aquila, A. / Botha, S. / Doak, R.B. / Koglin, J. / Liang, M. / Shoeman, R.L. / Williams, G. / Boutet, S. / Schlichting, I.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 57.740, 149.980
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-1 / 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.: 265 / 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

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6-0.8 M Na,K tartrate, 0.1 M Na Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.07 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 26126 / % possible obs: 97 % / Redundancy: 28.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 71.3
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.087 / % possible all: 61.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.134→20 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 16.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 1315 5.03 %
Rwork0.1292 --
obs0.1316 26124 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.134→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 265 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071625
X-RAY DIFFRACTIONf_angle_d1.0362194
X-RAY DIFFRACTIONf_dihedral_angle_d11.475577
X-RAY DIFFRACTIONf_chiral_restr0.042234
X-RAY DIFFRACTIONf_plane_restr0.004291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.134-2.21950.20991110.14662083X-RAY DIFFRACTION73
2.2195-2.32050.19111500.12942814X-RAY DIFFRACTION100
2.3205-2.44280.16141500.12652835X-RAY DIFFRACTION100
2.4428-2.59580.20151480.13512855X-RAY DIFFRACTION100
2.5958-2.79620.20571470.13622834X-RAY DIFFRACTION100
2.7962-3.07760.16021580.1332846X-RAY DIFFRACTION100
3.0776-3.52280.1691490.12682857X-RAY DIFFRACTION100
3.5228-4.43770.15341520.11322848X-RAY DIFFRACTION100
4.4377-45.76030.18231500.13562837X-RAY DIFFRACTION100

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