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- PDB-7ljv: X-ray radiation damage series on Thaumatin at 277K, crystal struc... -

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Basic information

Entry
Database: PDB / ID: 7ljv
TitleX-ray radiation damage series on Thaumatin at 277K, crystal structure, dataset 4
ComponentsThaumatin I
KeywordsPLANT PROTEIN / radiation damage / conformational heterogeneity
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsYabukarski, F. / Doukov, T. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.
Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D.
History
DepositionJan 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.830, 58.830, 151.270
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: 22243.119 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.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY
Sequence detailsThaumatin was purchased from Sigma and is a mixture of thaumatin I and thaumatin II and both are ...Thaumatin was purchased from Sigma and is a mixture of thaumatin I and thaumatin II and both are most likely present in the crystal. While thaumatin I (P02883) has an N at position 68 (precursor numbering), thaumatin II (P02884) has a K at the same position. Modeling either N or K is justified, in this case K explains the electron density better (better fit to map and better statistics).

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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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 24% Na K Tartrate (w/v), 15% ethylene glycol (v/v), and 0.1 M BisTris Propane

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.48→38.29 Å / Num. obs: 45300 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.21 Å2 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.066 / Net I/σ(I): 9.1
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 8 % / Rmerge(I) obs: 9.56 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2155 / Rpim(I) all: 3.509 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQW

1rqw


Resolution: 1.48→37.82 Å / SU ML: 0.1625 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1692 2225 5.06 %
Rwork0.1381 41747 -
obs0.1396 43972 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 1.48→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 143 1705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741813
X-RAY DIFFRACTIONf_angle_d0.92722490
X-RAY DIFFRACTIONf_chiral_restr0.0781258
X-RAY DIFFRACTIONf_plane_restr0.0062346
X-RAY DIFFRACTIONf_dihedral_angle_d14.0161679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.355970.31381809X-RAY DIFFRACTION68.46
1.51-1.550.30361250.28312304X-RAY DIFFRACTION87.88
1.55-1.590.29681380.24172590X-RAY DIFFRACTION98.63
1.59-1.630.29731470.22982633X-RAY DIFFRACTION99.61
1.63-1.680.25031460.2022617X-RAY DIFFRACTION99.71
1.68-1.730.19511470.1772647X-RAY DIFFRACTION99.93
1.73-1.790.23611210.16152643X-RAY DIFFRACTION99.93
1.79-1.860.17751440.13812651X-RAY DIFFRACTION99.93
1.86-1.950.16271480.11812650X-RAY DIFFRACTION100
1.95-2.050.15451330.09992688X-RAY DIFFRACTION100
2.05-2.180.11681350.09792704X-RAY DIFFRACTION99.93
2.18-2.350.14351710.10042657X-RAY DIFFRACTION100
2.35-2.590.13431440.10512705X-RAY DIFFRACTION100
2.59-2.960.1431440.10922730X-RAY DIFFRACTION100
2.96-3.730.1521420.11872767X-RAY DIFFRACTION99.93
3.73-37.820.1761430.16272952X-RAY DIFFRACTION99.84

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