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- PDB-5vky: Yeast Tda2 (YER071C) - a dynein light chain family member that wo... -

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Basic information

Entry
Database: PDB / ID: 5vky
TitleYeast Tda2 (YER071C) - a dynein light chain family member that works independently of the dynein motor complex and microtubules.
ComponentsTopoisomerase I damage affected protein 2
KeywordsPROTEIN BINDING / dynein light chain clathrin mediated endocytosis
Function / homologyDynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / cell projection / cytoplasm / Topoisomerase I damage affected protein 2
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcDonald, S.M. / Di Pietro, S.M. / Peersen, O.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1616775 United States
CitationJournal: J. Cell Biol. / Year: 2017
Title: Novel function of a dynein light chain in actin assembly during clathrin-mediated endocytosis.
Authors: Farrell, K.B. / McDonald, S. / Lamb, A.K. / Worcester, C. / Peersen, O.B. / Di Pietro, S.M.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Topoisomerase I damage affected protein 2
B: Topoisomerase I damage affected protein 2


Theoretical massNumber of molelcules
Total (without water)31,1512
Polymers31,1512
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-17 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.390, 161.259, 33.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Topoisomerase I damage affected protein 2


Mass: 15575.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain JAY291) (yeast)
Strain: JAY291 / Gene: TDA2, C1Q_03053 / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7GRQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5
Details: 1.6 M ammonium sulfate, 50 mM Bis-Tris, pH 5, 15% xylitol
PH range: 4.9-5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→53.75 Å / Num. obs: 12771 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.015 / Rrim(I) all: 0.038 / Net I/σ(I): 32.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.386.40.1958.412410.9860.0830.212100
8.91-53.755.30.01960.32690.9990.0090.02197.7

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.315 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 648 4.66 %Random
Rwork0.2119 ---
obs0.2143 12714 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.11 Å2 / Biso mean: 44.9667 Å2 / Biso min: 20.77 Å2
Refinement stepCycle: final / Resolution: 2.3→40.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 0 87 1930
Biso mean---47.72 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081868
X-RAY DIFFRACTIONf_angle_d0.8692518
X-RAY DIFFRACTIONf_chiral_restr0.052294
X-RAY DIFFRACTIONf_plane_restr0.005313
X-RAY DIFFRACTIONf_dihedral_angle_d3.1141150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.53150.26641620.211829623124
2.5315-2.89770.29311350.22529583093
2.8977-3.65050.25411550.220530123167
3.6505-40.32090.26271400.203831903330

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