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- PDB-6s1e: Structure of thaumatin determined at SwissFEL using native-SAD at... -

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Basic information

Entry
Database: PDB / ID: 6s1e
TitleStructure of thaumatin determined at SwissFEL using native-SAD at 6.06 keV from all available diffraction patterns
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / native-SAD / Serial femtosecond crystallography / SFX / SwissFEL / Jungfrau
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 / FREE ELECTRON LASER / SAD / Resolution: 1.95 Å
AuthorsNass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. ...Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, J.C.
CitationJournal: Iucrj / Year: 2020
Title: Advances in long-wavelength native phasing at X-ray free-electron lasers.
Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / ...Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Bacellar, C. / Bohinc, R. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, C.J.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.320, 58.320, 150.900
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 genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: 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.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 1.6 M potassium sodium tartrate tetrahydrate, 100 mM Na-HEPES

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 2.046 Å
DetectorType: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Aug 12, 2018 / Frequency: 25
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.046 Å / Relative weight: 1
ReflectionResolution: 1.95→24.39 Å / Num. obs: 36026 / % possible obs: 100 % / Redundancy: 1149 % / Net I/σ(I): 23.96
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2384
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→23.154 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.1681 1823 5.06 %
Rwork0.1441 --
obs0.1452 36026 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→23.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 54 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071614
X-RAY DIFFRACTIONf_angle_d0.8172197
X-RAY DIFFRACTIONf_dihedral_angle_d7.7261286
X-RAY DIFFRACTIONf_chiral_restr0.053234
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.44181400.45932593X-RAY DIFFRACTION97
2.0027-2.06160.31561340.2712577X-RAY DIFFRACTION98
2.0616-2.12810.22991380.22782583X-RAY DIFFRACTION98
2.1281-2.20410.23671430.21622629X-RAY DIFFRACTION99
2.2041-2.29230.19641390.18142666X-RAY DIFFRACTION100
2.2923-2.39650.22791380.18082635X-RAY DIFFRACTION100
2.3965-2.52270.2381460.18472638X-RAY DIFFRACTION100
2.5227-2.68050.25161420.1872644X-RAY DIFFRACTION100
2.6805-2.88710.20221420.18972655X-RAY DIFFRACTION100
2.8871-3.1770.2011440.18072651X-RAY DIFFRACTION100
3.177-3.63520.17151420.14242627X-RAY DIFFRACTION100
3.6352-4.57420.12831410.10652651X-RAY DIFFRACTION100
4.5742-23.15560.11281340.10422654X-RAY DIFFRACTION100

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