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- PDB-7o5k: Structure of thaumatin determined at SwissFEL using native-SAD at... -

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Entry
Database: PDB / ID: 7o5k
TitleStructure of thaumatin determined at SwissFEL using native-SAD at 6.02 keV with photon energy bandwidth of 2.15% and pinkIndexer with 30000 indexed images
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / native-SAD / large bandwidth / pink beam / SFX / serial crystallography / pinkIndexer
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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: 2.05 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 pinkIndexer with 30000 indexed images
Authors: Nass, K.
History
DepositionApr 8, 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

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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
Water1,40578
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)58.520, 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.: 78 / 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: 2.91 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: 2.05→23.14 Å / Num. obs: 31565 / % possible obs: 100 % / Redundancy: 356 % / Biso Wilson estimate: 43.04 Å2 / CC1/2: 0.997 / R split: 0.0458 / Net I/σ(I): 12.9
Reflection shellResolution: 2.05→2.1 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2114 / CC1/2: 0.218 / R split: 1.51 / % possible all: 92
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
CrystFELdata collection
CrystFELdata reduction
CrystFELdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→23.14 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1919 818 5 %
Rwork0.161 15551 -
obs0.1626 16369 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 78 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861605
X-RAY DIFFRACTIONf_angle_d0.99552179
X-RAY DIFFRACTIONf_chiral_restr0.0606234
X-RAY DIFFRACTIONf_plane_restr0.0118289
X-RAY DIFFRACTIONf_dihedral_angle_d6.515230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.4538970.3671854X-RAY DIFFRACTION69.18
2.18-2.350.27411400.23862650X-RAY DIFFRACTION99.54
2.35-2.580.24951410.20482680X-RAY DIFFRACTION99.93
2.58-2.960.24681420.19692709X-RAY DIFFRACTION99.93
2.96-3.720.20651450.16762746X-RAY DIFFRACTION99.93
3.72-23.140.13531530.12022912X-RAY DIFFRACTION99.77

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