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- PDB-1xdx: Solution Structure of the Tctex1 Light Chain From Chlamydomonas I... -

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Basic information

Entry
Database: PDB / ID: 1xdx
TitleSolution Structure of the Tctex1 Light Chain From Chlamydomonas Inner Dynein Arm I1
ComponentsTctex1 Light Chain protein
KeywordsCONTRACTILE PROTEIN / Chlamydomonas flagella / Tctex1 dimer / NMR solution structure
Function / homology
Function and homology information


cytoplasmic dynein complex / dynein intermediate chain binding / microtubule-based movement / identical protein binding / cytoplasm
Similarity search - Function
Tctex-1 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Ribosomal protein S3 C-terminal domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain Tctex1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsWu, H. / Maciejewski, M.W. / Takebe, S. / King, S.M.
CitationJournal: Structure / Year: 2005
Title: Solution Structure of the Tctex1 Dimer Reveals a Mechanism for Dynein-Cargo Interactions
Authors: Wu, H. / Maciejewski, M.W. / Takebe, S. / King, S.M.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tctex1 Light Chain protein
B: Tctex1 Light Chain protein


Theoretical massNumber of molelcules
Total (without water)25,3612
Polymers25,3612
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 90target function,structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Tctex1 Light Chain protein


Mass: 12680.427 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Description: flagella Inner Dynein Arm I1 / Gene: AF039437 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 cells / References: UniProt: O64980

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
1~0.7 mM tctex1 protein; U-15N,13C; 20 mM Na phosphate; pH 6.7; 100mM NaCl; 20mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
2~0.7 mM tctex1 protein; U-15N,13C; 20 mM Na phosphate; pH 6.7; 100mM NaCl; 20mM DTT; >99% D2O>99% D2O
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Bvariancollection
NMRPipe1.1Delaglio, F.processing
XEASY1.4Bartels, C.data analysis
CYANA1.1Guentert, P.structure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 90 / Conformers submitted total number: 15

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