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- PDB-7o51: Structure of thaumatin determined at SwissFEL using native-SAD at... -

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Basic information

Entry
Database: PDB / ID: 7o51
TitleStructure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and XGANDALF
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / thaumatin / SwissFEL / native-SAD / SASE / large bandwidth / pink
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 / SAD / Resolution: 2.2 Å
AuthorsNass, K.
CitationJournal: To Be Published
Title: Structure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and XGANDALF
Authors: Nass, K.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.520, 58.520, 151.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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.: 46 / 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: 57.79 %
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: 2.059 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.059 Å / Relative weight: 1
ReflectionResolution: 2.2→24.8 Å / Num. obs: 25539 / % possible obs: 100 % / Redundancy: 418 % / Biso Wilson estimate: 49.5 Å2 / CC1/2: 0.999 / R split: 0.038 / Net I/σ(I): 15.82
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1738 / CC1/2: 0.501 / R split: 0.8962 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
CrystFEL1.18.2_3874data scaling
CrystFEL1.18.2_3874data reduction
SHARPphasing
ARP/wARPmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→23.14 Å / SU ML: 0.2476 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1966 703 5 %
Rwork0.1528 13354 -
obs0.1549 14057 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 46 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991605
X-RAY DIFFRACTIONf_angle_d1.13012179
X-RAY DIFFRACTIONf_chiral_restr0.0592234
X-RAY DIFFRACTIONf_plane_restr0.0075289
X-RAY DIFFRACTIONf_dihedral_angle_d13.5984230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.30841370.23622597X-RAY DIFFRACTION100
2.37-2.610.2691380.20182610X-RAY DIFFRACTION100
2.61-2.980.26911380.19922640X-RAY DIFFRACTION100
2.98-3.760.21731410.17082673X-RAY DIFFRACTION99.96
3.76-23.140.15141490.11912834X-RAY DIFFRACTION99.97

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