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- PDB-7lnd: X-ray radiation damage series on Thaumatin at 277K, multi-conform... -

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Basic information

Entry
Database: PDB / ID: 7lnd
TitleX-ray radiation damage series on Thaumatin at 277K, multi-conformer model, dataset 4 (merged)
ComponentsThaumatin I
KeywordsPLANT PROTEIN / radiation damage / conformational heterogeneity
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: 1.22 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
DepositionFeb 6, 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 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Oct 16, 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
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.780, 58.780, 151.060
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.: 151 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
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: 1.22→38.27 Å / Num. obs: 79923 / % possible obs: 100 % / Redundancy: 163.6 % / Biso Wilson estimate: 17.54 Å2 / Rmerge(I) obs: 0.459 / Rpim(I) all: 0.036 / Net I/σ(I): 28.5
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 146.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3883 / Rpim(I) all: 4.793 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LFG

7lfg


Resolution: 1.22→37.76 Å / SU ML: 0.1225 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.0302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1485 3951 4.97 %
Rwork0.136 75547 -
obs0.1366 79498 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.89 Å2
Refinement stepCycle: LAST / Resolution: 1.22→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 151 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883677
X-RAY DIFFRACTIONf_angle_d1.08054983
X-RAY DIFFRACTIONf_chiral_restr0.0809540
X-RAY DIFFRACTIONf_plane_restr0.0074658
X-RAY DIFFRACTIONf_dihedral_angle_d12.50081339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.230.31111580.30932601X-RAY DIFFRACTION99.1
1.23-1.250.31941270.3092664X-RAY DIFFRACTION99.01
1.25-1.270.28031420.27642619X-RAY DIFFRACTION99.5
1.27-1.280.2491510.23712628X-RAY DIFFRACTION99.61
1.28-1.30.24631290.22392665X-RAY DIFFRACTION99.71
1.3-1.320.25831280.22172655X-RAY DIFFRACTION99.71
1.32-1.340.26221370.21032682X-RAY DIFFRACTION99.82
1.34-1.360.1971320.20342665X-RAY DIFFRACTION99.86
1.36-1.390.17251480.19142652X-RAY DIFFRACTION99.86
1.39-1.410.18931270.17782691X-RAY DIFFRACTION99.89
1.41-1.440.17421300.17272672X-RAY DIFFRACTION99.75
1.44-1.470.19431290.16092684X-RAY DIFFRACTION99.89
1.47-1.50.18331290.15442670X-RAY DIFFRACTION99.96
1.5-1.540.18481460.1472670X-RAY DIFFRACTION99.86
1.54-1.580.14761400.13272678X-RAY DIFFRACTION99.86
1.58-1.620.15381440.12682673X-RAY DIFFRACTION99.93
1.62-1.670.14261530.12212675X-RAY DIFFRACTION99.96
1.67-1.720.13661490.11762680X-RAY DIFFRACTION99.82
1.72-1.780.12431300.11692728X-RAY DIFFRACTION99.93
1.78-1.850.13621440.11322679X-RAY DIFFRACTION99.93
1.85-1.940.13181510.11382695X-RAY DIFFRACTION100
1.94-2.040.13091330.10472742X-RAY DIFFRACTION100
2.04-2.170.11511350.10842722X-RAY DIFFRACTION100
2.17-2.330.12181750.10812711X-RAY DIFFRACTION100
2.33-2.570.12171490.11652747X-RAY DIFFRACTION100
2.57-2.940.12931460.11842779X-RAY DIFFRACTION100
2.94-3.70.13511440.12282812X-RAY DIFFRACTION99.93
3.7-37.760.17161450.16083008X-RAY DIFFRACTION99.9

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