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- PDB-6s1g: Structure of thaumatin determined at SwissFEL using native-SAD at... -

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Basic information

Entry
Database: PDB / ID: 6s1g
TitleStructure of thaumatin determined at SwissFEL using native-SAD at 6.06 keV from 50,000 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: 2 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 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.group_PDB ..._atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area9580 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: isolated from a natural source / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2→23.15 Å / Num. obs: 31191 / % possible obs: 100 % / Redundancy: 188 % / Net I/σ(I): 11.81
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2155
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→23.15 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74
RfactorNum. reflection% reflection
Rfree0.1692 1698 5.06 %
Rwork0.1393 --
obs0.1408 33556 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→23.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 15 88 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081605
X-RAY DIFFRACTIONf_angle_d0.9782179
X-RAY DIFFRACTIONf_dihedral_angle_d8.0281286
X-RAY DIFFRACTIONf_chiral_restr0.051234
X-RAY DIFFRACTIONf_plane_restr0.006289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05880.30241360.29942627X-RAY DIFFRACTION100
2.0588-2.12520.31131400.22872667X-RAY DIFFRACTION100
2.1252-2.20110.23031370.19842638X-RAY DIFFRACTION100
2.2011-2.28920.19951460.1772684X-RAY DIFFRACTION100
2.2892-2.39330.24761390.17352630X-RAY DIFFRACTION100
2.3933-2.51930.21691470.17272673X-RAY DIFFRACTION100
2.5193-2.67690.23411420.1712647X-RAY DIFFRACTION100
2.6769-2.88330.21571440.17432658X-RAY DIFFRACTION100
2.8833-3.17280.1941440.16272671X-RAY DIFFRACTION100
3.1728-3.63040.16581410.12652651X-RAY DIFFRACTION100
3.6304-4.56810.12661430.10242649X-RAY DIFFRACTION100
4.5681-23.15550.11381390.10632663X-RAY DIFFRACTION100

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