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- PDB-6srj: X-ray pump X-ray probe on thaumatin nanocrystals: single pulse re... -

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Basic information

Entry
Database: PDB / ID: 6srj
TitleX-ray pump X-ray probe on thaumatin nanocrystals: single pulse reference data
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Radiation damage / SERIAL femtosecond CRYSTALLOGRAPHY / X-ray FREE-ELECTRON LASER / time-resolved crystallography
Function / homology
Function and homology information


cytoplasmic vesicle
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKloos, M. / Gorel, A. / Nass, K.
CitationJournal: Nat Commun / Year: 2020
Title: Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.
Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / ...Authors: Nass, K. / Gorel, A. / Abdullah, M.M. / V Martin, A. / Kloos, M. / Marinelli, A. / Aquila, A. / Barends, T.R.M. / Decker, F.J. / Bruce Doak, R. / Foucar, L. / Hartmann, E. / Hilpert, M. / Hunter, M.S. / Jurek, Z. / Koglin, J.E. / Kozlov, A. / Lutman, A.A. / Kovacs, G.N. / Roome, C.M. / Shoeman, R.L. / Santra, R. / Quiney, H.M. / Ziaja, B. / Boutet, S. / Schlichting, I.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.849, 57.849, 150.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.47 Å3/Da / Density % sol: 50.19 % / Description: nanocrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: 0.8 M NA, K TARTRATE, 0.1 M NA HEPES PH 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.75 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.32→23 Å / Num. obs: 11104 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.973 / R split: 0.09 / Net I/σ(I): 7.4
Reflection shellResolution: 2.32→2.36 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 850 / CC1/2: 0.973 / R split: 0.222
Serial crystallography measurementFocal spot size: 0.025 µm2 / Pulse duration: 15 fsec. / Pulse energy: 500 µJ / Pulse photon energy: 7.07 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: GDVN injection / Method: injection
Serial crystallography data reductionFrames indexed: 11000 / Lattices indexed: 11000

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fgt

5fgt


Resolution: 2.3→23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.829 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The submitted coordinates represent the mean of 100 coordinate sets obtained by refining against 100 different integrated diffraction intensity datasets obtained by jackknife resampling of the diffraction snapshots. The coordinate header originates from one of the individual refinements. Cysteine residues were modeled as alanines and non-covalently attached sulphur atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 895 7.5 %RANDOM
Rwork0.1382 ---
obs0.1405 11104 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.18 Å2 / Biso mean: 26.368 Å2 / Biso min: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0 Å2
2--0.29 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 2.3→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 97 1657
Biso mean--24.37 29.88 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171433
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.6592173
X-RAY DIFFRACTIONr_angle_other_deg1.4741.5843316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0975210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47421.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65815227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5441512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 60 -
Rwork0.184 790 -
all-850 -
obs--100 %

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