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- PDB-2jml: Solution structure of the N-terminal domain of CarA repressor -

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Basic information

Entry
Database: PDB / ID: 2jml
TitleSolution structure of the N-terminal domain of CarA repressor
ComponentsDNA BINDING DOMAIN/TRANSCRIPTIONAL REGULATOR
KeywordsTRANSCRIPTION / anti-repressor / MerR / carotenogenesis
Function / homology
Function and homology information


cobalamin binding / regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Methionine synthase domain / MerR HTH family regulatory protein / B12 binding domain / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Cobalamin-binding domain superfamily ...Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Methionine synthase domain / MerR HTH family regulatory protein / B12 binding domain / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
B12 binding domain/transcriptional regulator, MerR family
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJimenez, M. / Padmanabhan, S. / Gonzalez, C. / Perez-Marin, M.C. / Elias-Arnanz, M. / Murillo, F.J. / Rico, M.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor.
Authors: Navarro-Aviles, G. / Jimenez, M.A. / Perez-Marin, M.C. / Gonzalez, C. / Rico, M. / Murillo, F.J. / Elias-Arnanz, M. / Padmanabhan, S.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.deposit_site / _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: DNA BINDING DOMAIN/TRANSCRIPTIONAL REGULATOR


Theoretical massNumber of molelcules
Total (without water)9,4721
Polymers9,4721
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 / 20all calculated structures submitted
RepresentativeModel #1fewest number of violations

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Components

#1: Protein DNA BINDING DOMAIN/TRANSCRIPTIONAL REGULATOR


Mass: 9471.791 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1DDV9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1233D 1H-15N NOESY
1333D 1H-15N TOCSY
1432D 1H-1H NOESY
1532D 1H-1H TOCSY
1612D 1H-1H NOESY
1712D 1H-1H TOCSY
1812D 1H-1H COSY
1922D 1H-1H NOESY
11022D 1H-1H TOCSY
11122D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM CarA(Nter), 0.2 mM DSS, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O, 10% D2O90% H2O/10% D2O
20.8 mM CarA(Nter), 0.2 mM DSS, 100 mM sodium chloride, 50 mM sodium phosphate, 100% D2O100% D2O
30.8 mM [U-100% 15N] CarA(Nter), 0.2 mM DSS, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCarA(Nter)1
90 %H2O1
10 %D2O1
0.1 mMDSS1
100 mMsodium chloride1
50 mMsodium phosphate1
0.5 mMCarA(Nter)2
100 %D2O2
0.1 mMDSS2
100 mMsodium chloride2
50 mMsodium phosphate2
0.5 mMCarA(Nter)[U-100% 15N]3
90 %H2O3
10 %D2O3
0.1 mMDSS3
100 mMsodium chloride3
50 mMsodium phosphate3
Sample conditionsIonic strength: 0.150 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1Guntert, Mumenthaler and Wuthrichsolution structure
CYANA1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Cyana 1.0
NMR representativeSelection criteria: fewest number of violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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