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- PDB-2kss: NMR structure of Myxococcus xanthus antirepressor CarS1 -

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Basic information

Entry
Database: PDB / ID: 2kss
TitleNMR structure of Myxococcus xanthus antirepressor CarS1
ComponentsCarotenogenesis protein carS
KeywordsTRANSCRIPTION REGULATOR / protein / antirepressor / Activator / Carotenoid biosynthesis / Transcription / Transcription regulation
Function / homologySH3 type barrels. - #630 / Antirepressor CarS / CarS, SH3 domain / CarS bacterial SH3 domain / carotenoid biosynthetic process / SH3 type barrels. / Roll / Mainly Beta / Antirepressor protein CarS
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJimenez, M. / Gonzalez, C. / Padmanabhan, S. / Leon, E. / Navarro-Aviles, G. / Elias-Arnanz, M.
Citation
Journal: Nucleic Acids Res. / Year: 2010
Title: A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix.
Authors: Leon, E. / Navarro-Aviles, G. / Santiveri, C.M. / Flores-Flores, C. / Rico, M. / Gonzalez, C. / Murillo, F.J. / Elias-Arnanz, M. / Jimenez, M.A. / Padmanabhan, S.
#1: Journal: BIOMOL.NMR ASSIGN. / Year: 2009
Title: 1H, 13C, 15N backbone and side chain resonance assignments of a Myxococcus xanthus antirepressor with no known sequence homologues
Authors: Leon, E. / Navarro-Aviles, G. / Flores, C. / Elias-Arnanz, M. / Gonzalez, C. / Jimenez, M. / Padmanabhan, S.
History
DepositionJan 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenogenesis protein carS


Theoretical massNumber of molelcules
Total (without water)11,4891
Polymers11,4891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Carotenogenesis protein carS


Mass: 11488.879 Da / Num. of mol.: 1 / Fragment: CarS1 (UNP residues 1-86)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: carS / Production host: Escherichia coli (E. coli) / References: UniProt: Q06911

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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 CBCANH
1313D CBCA(CO)NH
1413D HNCA
1513D HNCO
1613D HBHANH
1713D HA(CA)NH
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11022D 1H-13C HSQC
11123D (H)CCH-TOCSY
11223D 1H-13C NOESY
11332D 1H-15N HSQC
11433D HNHA
11533D 1H-15N NOESY
11642D 1H-1H COSY
11742D 1H-1H TOCSY
11842D 1H-1H NOESY
11952D 1H-1H COSY
12052D 1H-1H TOCSY
12152D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] CarS1, 90 % H2O, 10 % [U-99% 2H] D2O, 50 mM sodium phosphate, 1 mM DTT, 0.1 mM sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] CarS1, 100 % [U-99% 2H] D2O, 50 mM sodium phosphate, 1 mM DTT, 0.1 mM sodium azide, 0.2 mM DSS, 100% D2O100% D2O
31 mM [U-100% 15N] CarS1, 90 % H2O, 10 % [U-99% 2H] D2O, 50 mM sodium phosphate, 1 mM DTT, 0.1 mM sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41 mM CarS1, 90 % H2O, 10 % [U-99% 2H] D2O, 50 mM sodium phosphate, 1 mM DTT, 0.1 mM sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
51 mM CarS1, 100 % [U-99% 2H] D2O, 50 mM sodium phosphate, 1 mM DTT, 0.1 mM sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCarS1[U-100% 13C; U-100% 15N]1
90 %H2O1
10 %D2O[U-99% 2H]1
50 mMsodium phosphate1
1 mMDTT1
0.1 mMsodium azide1
0.2 mMDSS1
1 mMCarS1[U-100% 13C; U-100% 15N]2
100 %D2O[U-99% 2H]2
50 mMsodium phosphate2
1 mMDTT2
0.1 mMsodium azide2
0.2 mMDSS2
1 mMCarS1[U-100% 15N]3
90 %H2O3
10 %D2O[U-99% 2H]3
50 mMsodium phosphate3
1 mMDTT3
0.1 mMsodium azide3
0.2 mMDSS3
1 mMCarS14
90 %H2O4
10 %D2O[U-99% 2H]4
50 mMsodium phosphate4
1 mMDTT4
0.1 mMsodium azide4
0.2 mMDSS4
1 mMCarS15
100 %D2O[U-99% 2H]5
50 mMsodium phosphate5
1 mMDTT5
0.1 mMsodium azide5
0.2 mMDSS5
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298.4 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdihedral angle restraints
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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