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- PDB-2m1u: Solution structure of the small dictyostelium discoideium myosin ... -

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Basic information

Entry
Database: PDB / ID: 2m1u
TitleSolution structure of the small dictyostelium discoideium myosin light chain mlcb provides insights into iq-motif recognition of class i myosin myo1b
Componentsmyosin light chain MlcB
KeywordsCONTRACTILE PROTEIN / Myosin light chain
Function / homologyEF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 21
Model type detailsminimized average
AuthorsLiburd, J. / Chitayat, S. / Crawley, S.W. / Denis, C.M. / Cote, G.P. / Smith, S.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of the small Dictyostelium discoideum myosin light chain MlcB provides insights into MyoB IQ motif recognition.
Authors: Liburd, J. / Chitayat, S. / Crawley, S.W. / Munro, K. / Miller, E. / Denis, C.M. / Spencer, H.L. / Cote, G.P. / Smith, S.P.
History
DepositionDec 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: myosin light chain MlcB


Theoretical massNumber of molelcules
Total (without water)10,4711
Polymers10,4711
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)21 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein myosin light chain MlcB


Mass: 10471.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1923D 1H-13C NOESY aromatic
11013D 1H-15N NOESY
11113D H(CCO)NH
11223D 1H-13C NOESY aliphatic
11322D 1H-1H NOESY
11422D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] MlcB, 10 mM HEPES, 50 mM sodium chloride, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] MlcB, 10 mM HEPES, 50 mM sodium chloride, 0.5 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMlcB-1[U-100% 13C; U-100% 15N]1
10 mMHEPES-21
50 mMsodium chloride-31
0.5 mMDSS-41
1 mMMlcB-5[U-100% 13C; U-100% 15N]2
10 mMHEPES-62
50 mMsodium chloride-72
0.5 mMDSS-82
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 21

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