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- PDB-8rs3: Thaumatin measured via serial crystallography from a kapton HARE-... -

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Basic information

Entry
Database: PDB / ID: 8rs3
TitleThaumatin measured via serial crystallography from a kapton HARE-chip (50 micron)
ComponentsThaumatin I
KeywordsSUGAR BINDING PROTEIN / thaumatin / serial crystallography / SSX / Kapton HARE-chip
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
CitationJournal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Schulz, E.C.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6292
Polymers25,4791
Non-polymers1501
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.200, 58.200, 150.900
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 I / Thaumatin-1


Mass: 25478.957 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.: 127 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: batch mode
Details: Microcrystals were formed via mixing protein solution with precipitant solution, 0.1mM KH2PO4 pH 6.5, 1.7M sodium tartrate with a 1:3 ratio respectively.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→54.3 Å / Num. obs: 29556 / % possible obs: 100 % / Redundancy: 180.5 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.982 / CC star: 0.996 / R split: 0.123 / Net I/σ(I): 5.93
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2868 / CC1/2: 0.497 / CC star: 0.815 / R split: 0.942
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: HARE-chip, Kapton
Serial crystallography data reductionFrames indexed: 16466 / Lattices indexed: 20325

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→54.3 Å / SU ML: 0.2176 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 1384 4.7 %
Rwork0.1625 28066 -
obs0.1635 29450 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→54.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 10 127 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621620
X-RAY DIFFRACTIONf_angle_d0.87422198
X-RAY DIFFRACTIONf_chiral_restr0.0555234
X-RAY DIFFRACTIONf_plane_restr0.0083292
X-RAY DIFFRACTIONf_dihedral_angle_d6.5758232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.37831540.35112740X-RAY DIFFRACTION99.76
1.76-1.830.27781320.26322742X-RAY DIFFRACTION99.79
1.83-1.910.26761350.21232741X-RAY DIFFRACTION99.86
1.91-2.020.21841280.19062753X-RAY DIFFRACTION99.9
2.02-2.140.19431550.17032760X-RAY DIFFRACTION99.97
2.14-2.310.19331230.162791X-RAY DIFFRACTION100
2.31-2.540.19421500.16232790X-RAY DIFFRACTION100
2.54-2.910.2441160.17352843X-RAY DIFFRACTION99.93
2.91-3.660.15831500.14862853X-RAY DIFFRACTION99.97
3.66-54.30.11721410.12273053X-RAY DIFFRACTION99.97

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