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- PDB-9eqt: 24fs pulse duration 10uJ pulse energy thaumatin -

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Basic information

Entry
Database: PDB / ID: 9eqt
Title24fs pulse duration 10uJ 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: 1.49 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

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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
Water2,576143
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

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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.: 143 / 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: 1.49→32 Å / Num. obs: 44873 / % possible obs: 100 % / Redundancy: 116.1 % / CC1/2: 0.948 / R split: 0.173 / Net I/σ(I): 4.65
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 2222 / CC1/2: 0.3 / R split: 1.356
Serial crystallography measurementFocal spot size: 7.98 µm2 / Pulse duration: 24 fsec. / Pulse energy: 10 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: 12305

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFEL10.2data reduction
CrystFEL10.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.41 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2068 2258 5.043 %
Rwork0.1776 42514 -
all0.179 --
obs-44772 99.967 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.315 Å2-0 Å2-0 Å2
2--0.315 Å2-0 Å2
3----0.629 Å2
Refinement stepCycle: LAST / Resolution: 1.49→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 143 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161483
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.812269
X-RAY DIFFRACTIONr_angle_other_deg0.6131.7563444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.344513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87210255
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1951070
X-RAY DIFFRACTIONr_chiral_restr0.0920.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_nbd_refined0.2150.2268
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21341
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2821
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.287
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.25
X-RAY DIFFRACTIONr_nbd_other0.1610.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.26
X-RAY DIFFRACTIONr_mcbond_it2.0932.067843
X-RAY DIFFRACTIONr_mcbond_other2.0452.065843
X-RAY DIFFRACTIONr_mcangle_it3.0723.7071057
X-RAY DIFFRACTIONr_mcangle_other3.0833.7091058
X-RAY DIFFRACTIONr_scbond_it3.4292.441815
X-RAY DIFFRACTIONr_scbond_other3.4312.442814
X-RAY DIFFRACTIONr_scangle_it5.1964.2931202
X-RAY DIFFRACTIONr_scangle_other5.1964.2931202
X-RAY DIFFRACTIONr_lrange_it6.53823.6151808
X-RAY DIFFRACTIONr_lrange_other6.43522.5811795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.5180.3681570.3733081X-RAY DIFFRACTION100
1.518-1.560.3481630.3293004X-RAY DIFFRACTION100
1.56-1.6050.2761470.2862922X-RAY DIFFRACTION100
1.605-1.6540.241490.2542857X-RAY DIFFRACTION100
1.654-1.7080.2641670.222731X-RAY DIFFRACTION100
1.708-1.7680.2361600.1972669X-RAY DIFFRACTION100
1.768-1.8350.1981360.1722580X-RAY DIFFRACTION100
1.835-1.9090.2161190.1722480X-RAY DIFFRACTION100
1.909-1.9940.1971280.1612405X-RAY DIFFRACTION100
1.994-2.0910.1711140.1532317X-RAY DIFFRACTION100
2.091-2.2030.1921180.1622172X-RAY DIFFRACTION100
2.203-2.3360.1791030.1592109X-RAY DIFFRACTION100
2.336-2.4970.156910.1541970X-RAY DIFFRACTION100
2.497-2.6950.2221100.1651820X-RAY DIFFRACTION100
2.695-2.9510.196900.171714X-RAY DIFFRACTION100
2.951-3.2950.197750.1641554X-RAY DIFFRACTION100
3.295-3.7980.171860.1461372X-RAY DIFFRACTION100
3.798-4.6360.157530.1381211X-RAY DIFFRACTION100
4.636-6.4880.225540.17961X-RAY DIFFRACTION100
6.488-320.318380.315585X-RAY DIFFRACTION98.7322

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