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- PDB-9equ: 24fs pulse duration 100uJ pulse energy thaumatin -

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Basic information

Entry
Database: PDB / ID: 9equ
Title24fs pulse duration 100uJ pulse energy thaumatin
ComponentsThaumatin I
KeywordsPLANT PROTEIN / radiation damage / XFEL / pulse duration and intensity / disulphides
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsOwen, R.L. / Hough, M.A. / Worrall, J. / Williams, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2025
Title: Damage before destruction? X-ray-induced changes in single-pulse serial femtosecond crystallography.
Authors: Williams, L.J. / Thompson, A.J. / Dijkstal, P. / Appleby, M. / Assmann, G. / Dworkowski, F.S.N. / Hiller, N. / Huang, C.Y. / Mason, T. / Perrett, S. / Prat, E. / Voulot, D. / Pedrini, B. / ...Authors: Williams, L.J. / Thompson, A.J. / Dijkstal, P. / Appleby, M. / Assmann, G. / Dworkowski, F.S.N. / Hiller, N. / Huang, C.Y. / Mason, T. / Perrett, S. / Prat, E. / Voulot, D. / Pedrini, B. / Beale, J.H. / Hough, M.A. / Worrall, J.A.R. / Owen, R.L.
History
DepositionMar 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)22,3782
Polymers22,2281
Non-polymers1501
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 58.500, 151.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 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.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 100 mg of thaumatin (Sigma-T7638) was dissolved in 1 ml of MiniQ water, reaching a concentration of 100 mg/ml with solutions vortexed to ensure complete dissolution. Subsequently, 200 uL of ...Details: 100 mg of thaumatin (Sigma-T7638) was dissolved in 1 ml of MiniQ water, reaching a concentration of 100 mg/ml with solutions vortexed to ensure complete dissolution. Subsequently, 200 uL of the thaumatin solution was mixed with 200 ul of 1.6 M (Na, K, tartrate) crystallization solution

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESC / Wavelength: 1.0306 Å
DetectorType: PSI JUNGFRAU 8M / Detector: PIXEL / Date: Sep 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0306 Å / Relative weight: 1
ReflectionResolution: 1.27→32 Å / Num. obs: 71976 / % possible obs: 100 % / Redundancy: 295.1 % / Biso Wilson estimate: 22.15 Å2 / CC1/2: 0.963 / R split: 0.154 / Net I/σ(I): 5.07
Reflection shellResolution: 1.27→1.29 Å / Num. unique obs: 3542 / CC1/2: 0.353 / R split: 1.328
Serial crystallography measurementFocal spot size: 7.98 µm2 / Pulse duration: 24 fsec. / Pulse energy: 100 µJ / Pulse photon energy: 12.03 keV / XFEL pulse repetition rate: 100 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: thin film / Sample holding: polymer fixed target
Serial crystallography data reductionFrames indexed: 17473

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL10.2data reduction
CrystFEL10.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→21.53 Å / SU ML: 0.1634 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 3282 5.01 %
Rwork0.1901 62179 -
obs0.191 65461 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.51 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 185 1740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531658
X-RAY DIFFRACTIONf_angle_d0.85492266
X-RAY DIFFRACTIONf_chiral_restr0.0792244
X-RAY DIFFRACTIONf_plane_restr0.0092302
X-RAY DIFFRACTIONf_dihedral_angle_d6.0504249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.35251420.3672630X-RAY DIFFRACTION99.75
1.32-1.340.34751410.33062654X-RAY DIFFRACTION99.82
1.34-1.360.32621370.28522669X-RAY DIFFRACTION99.75
1.36-1.390.25851400.25782625X-RAY DIFFRACTION99.75
1.39-1.410.27431460.24422647X-RAY DIFFRACTION99.96
1.41-1.440.23361480.22612677X-RAY DIFFRACTION99.89
1.44-1.470.24821440.232662X-RAY DIFFRACTION99.93
1.47-1.50.23881260.23542682X-RAY DIFFRACTION99.93
1.5-1.530.2491320.24432682X-RAY DIFFRACTION99.89
1.53-1.570.20721460.21332656X-RAY DIFFRACTION100
1.57-1.610.20421390.19482678X-RAY DIFFRACTION100
1.61-1.660.18911640.17642664X-RAY DIFFRACTION99.96
1.66-1.720.16481430.16922677X-RAY DIFFRACTION100
1.72-1.780.19521320.17362703X-RAY DIFFRACTION100
1.78-1.850.2071340.18492689X-RAY DIFFRACTION100
1.85-1.930.20361380.18382723X-RAY DIFFRACTION100
1.93-2.030.1721400.16362707X-RAY DIFFRACTION100
2.03-2.160.17581610.16562703X-RAY DIFFRACTION100
2.16-2.330.20261390.16622726X-RAY DIFFRACTION100
2.33-2.560.18091560.17422746X-RAY DIFFRACTION100
2.56-2.930.20921520.17742772X-RAY DIFFRACTION100
2.93-3.690.18871400.1742811X-RAY DIFFRACTION100
3.69-21.530.26021420.22352996X-RAY DIFFRACTION99.9

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