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- PDB-9er0: 53fs pulse duration 50uJ pulse energy thaumatin -

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Basic information

Entry
Database: PDB / ID: 9er0
Title53fs pulse duration 50uJ 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: 1.44 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

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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
Water3,297183
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.: 183 / 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 / 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: 1.44→32 Å / Num. obs: 49611 / % possible obs: 100 % / Redundancy: 195.7 % / CC1/2: 0.954 / R split: 0.167 / Net I/σ(I): 4.98
Reflection shellResolution: 1.44→1.47 Å / Num. unique obs: 2416 / CC1/2: 0.37 / R split: 1.245
Serial crystallography measurementFocal spot size: 7.98 µm2 / Pulse duration: 53 fsec. / Pulse energy: 50 µJ / Pulse photon energy: 12.03 keV / XFEL pulse repetition rate: 100 Hz
Serial crystallography sample deliveryDescription: polymer fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: thin film / Sample holding: polymer fixed target
Serial crystallography data reductionFrames indexed: 15947

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFEL10.2data reduction
CrystFEL10.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→32 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.156 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1902 2464 4.977 %
Rwork0.1645 47041 -
all0.166 --
obs-49505 99.962 %
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: 21.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.355 Å2-0 Å2-0 Å2
2--0.355 Å2-0 Å2
3----0.711 Å2
Refinement stepCycle: LAST / Resolution: 1.44→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 183 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121664
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161486
X-RAY DIFFRACTIONr_angle_refined_deg1.841.8092279
X-RAY DIFFRACTIONr_angle_other_deg0.6371.7583453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.209513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83310256
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3421071
X-RAY DIFFRACTIONr_chiral_restr0.0980.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2140.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21322
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2831
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2610.25
X-RAY DIFFRACTIONr_nbd_other0.1830.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.310.29
X-RAY DIFFRACTIONr_mcbond_it2.1131.991845
X-RAY DIFFRACTIONr_mcbond_other2.0531.988845
X-RAY DIFFRACTIONr_mcangle_it3.1593.5711060
X-RAY DIFFRACTIONr_mcangle_other3.1853.5731061
X-RAY DIFFRACTIONr_scbond_it3.5132.379819
X-RAY DIFFRACTIONr_scbond_other3.5152.38818
X-RAY DIFFRACTIONr_scangle_it5.3664.1631208
X-RAY DIFFRACTIONr_scangle_other5.3664.1631208
X-RAY DIFFRACTIONr_lrange_it6.94723.021836
X-RAY DIFFRACTIONr_lrange_other6.80520.9231807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.4670.3381760.3793415X-RAY DIFFRACTION100
1.467-1.5070.3111680.3273316X-RAY DIFFRACTION100
1.507-1.5510.2931450.2753251X-RAY DIFFRACTION100
1.551-1.5980.2221670.2393155X-RAY DIFFRACTION100
1.598-1.6510.2661570.2093056X-RAY DIFFRACTION100
1.651-1.7080.2181760.1872940X-RAY DIFFRACTION100
1.708-1.7730.21700.1682855X-RAY DIFFRACTION100
1.773-1.8450.1841400.1582750X-RAY DIFFRACTION100
1.845-1.9270.1861360.1562658X-RAY DIFFRACTION100
1.927-2.020.1751320.1422554X-RAY DIFFRACTION100
2.02-2.1290.1421390.1412402X-RAY DIFFRACTION100
2.129-2.2580.1791040.1422327X-RAY DIFFRACTION100
2.258-2.4130.1421020.1372172X-RAY DIFFRACTION100
2.413-2.6050.1611060.142035X-RAY DIFFRACTION100
2.605-2.8520.1871090.1511882X-RAY DIFFRACTION100
2.852-3.1850.192880.1491723X-RAY DIFFRACTION100
3.185-3.6720.17870.1391523X-RAY DIFFRACTION100
3.672-4.4820.117620.1271325X-RAY DIFFRACTION100
4.482-6.2770.199570.161057X-RAY DIFFRACTION100
6.277-320.333430.307645X-RAY DIFFRACTION98.2857

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