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- PDB-9eqy: 41fs pulse duration 100uJ pulse energy thaumatin -

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Basic information

Entry
Database: PDB / ID: 9eqy
Title41fs 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: 1.37 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
Water3,315184
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.: 184 / 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: 1.37→32 Å / Num. obs: 57471 / % possible obs: 100 % / Redundancy: 202.8 % / CC1/2: 0.942 / R split: 0.192 / Net I/σ(I): 4.36
Reflection shellResolution: 1.37→1.4 Å / Num. unique obs: 2785 / CC1/2: 0.36 / R split: 0.97
Serial crystallography measurementFocal spot size: 7.98 µm2 / Pulse duration: 41 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: 14706

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFEL10.2data reduction
CrystFEL10.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 0.945 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2084 2851 4.971 %
Rwork0.186 54502 -
all0.187 --
obs-57353 99.96 %
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: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.333 Å2-0 Å2-0 Å2
2--0.333 Å2-0 Å2
3----0.666 Å2
Refinement stepCycle: LAST / Resolution: 1.37→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 184 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161486
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.8092279
X-RAY DIFFRACTIONr_angle_other_deg0.6151.7583453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.186513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04410256
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.0221071
X-RAY DIFFRACTIONr_chiral_restr0.0930.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2180.2253
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21312
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2822
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2670.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.25
X-RAY DIFFRACTIONr_nbd_other0.1410.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.26
X-RAY DIFFRACTIONr_mcbond_it1.9691.946845
X-RAY DIFFRACTIONr_mcbond_other1.9121.944845
X-RAY DIFFRACTIONr_mcangle_it2.9273.4951060
X-RAY DIFFRACTIONr_mcangle_other2.9483.4971061
X-RAY DIFFRACTIONr_scbond_it3.0362.295819
X-RAY DIFFRACTIONr_scbond_other3.0382.296818
X-RAY DIFFRACTIONr_scangle_it4.6954.0371208
X-RAY DIFFRACTIONr_scangle_other4.6954.0371208
X-RAY DIFFRACTIONr_lrange_it6.45121.5351827
X-RAY DIFFRACTIONr_lrange_other6.24320.0811799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.3950.3872050.3653941X-RAY DIFFRACTION99.9759
1.395-1.4330.3421850.3323862X-RAY DIFFRACTION100
1.433-1.4750.311900.2833785X-RAY DIFFRACTION100
1.475-1.520.2731840.2433610X-RAY DIFFRACTION100
1.52-1.570.21850.213553X-RAY DIFFRACTION100
1.57-1.6250.2121770.1933478X-RAY DIFFRACTION100
1.625-1.6860.2071820.1713282X-RAY DIFFRACTION100
1.686-1.7550.1931940.1573169X-RAY DIFFRACTION100
1.755-1.8320.1681650.1523071X-RAY DIFFRACTION100
1.832-1.9220.1841440.1532960X-RAY DIFFRACTION100
1.922-2.0250.1741490.1452806X-RAY DIFFRACTION100
2.025-2.1470.151470.1482661X-RAY DIFFRACTION100
2.147-2.2950.1811130.1532543X-RAY DIFFRACTION100
2.295-2.4780.1611160.1422358X-RAY DIFFRACTION100
2.478-2.7130.1981260.1542163X-RAY DIFFRACTION100
2.713-3.030.1771010.1662004X-RAY DIFFRACTION100
3.03-3.4940.201980.1631764X-RAY DIFFRACTION100
3.494-4.2660.152820.1681527X-RAY DIFFRACTION100
4.266-5.980.276600.2471229X-RAY DIFFRACTION99.9225
5.98-320.437480.419736X-RAY DIFFRACTION98.2456

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