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- PDB-2jsc: NMR structure of the cadmium metal-sensor CMTR from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 2jsc
TitleNMR structure of the cadmium metal-sensor CMTR from Mycobacterium tuberculosis
ComponentsTranscriptional regulator Rv1994c/MT2050
KeywordsTRANSCRIPTION / CADMIUM / TRANSCRIPTIONAL REPRESSOR / SOLUTION STRUCTURE / STRUCTURAL GENOMICS / STRUCTURAL PROTEOMICS IN EUROPE / SPINE
Function / homology
Function and homology information


cadmium ion sensor activity / lead ion binding / cadmium ion binding / response to cadmium ion / response to lead ion / regulation of gene expression / DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / HTH-type transcriptional regulator CmtR / HTH-type transcriptional regulator CmtR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION
AuthorsBanci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. / Cavet, J.S. / Dennison, C. / Graham, A.I. / Harvie, D.R. / Robinson, N.J. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: NMR Structural Analysis of Cadmium Sensing by Winged Helix Repressor CmtR.
Authors: Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. / Cavet, J.S. / Dennison, C. / Graham, A.I. / Harvie, D.R. / Robinson, N.J.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator Rv1994c/MT2050
B: Transcriptional regulator Rv1994c/MT2050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2444
Polymers25,0192
Non-polymers2252
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Transcriptional regulator Rv1994c/MT2050


Mass: 12509.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1994c, MT2050, MTCY39.25 / Plasmid: pET29A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67731, UniProt: P9WMI9*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
131HNCA
141HN(CO)CA
151CBCA(CO)NH
161HNCO
1713D 13C- SEPARATED NOESY
181CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR, 1 mM [U-100% 15N] CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR, 1 mM [U-13C; U-15N] CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL ...Contents: 1 mM CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR, 1 mM [U-100% 15N] CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR, 1 mM [U-13C; U-15N] CMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR1
1 mMCMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR[U-100% 15N]2
1 mMCMTR, CADMIUM-RESPONSIVE TRANSCRIPTIONAL REGULATOR[U-13C; U-15N]3
Sample conditionsIonic strength: 50 Phosphate, 50 NaCl / pH: 7 / Pressure: ambient / Temperature: 312 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE5001
BRUKER AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, D.A. et al.refinement
XwinNMR3.1Bruker Biospinprocessing
XEASY1.3Bartels et al.chemical shift assignment
XEASY1.3Bartels et al.data analysis
CARA1.4Keller and Wuthrichdata analysis
CYANA1.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION
Software ordinal: 1
Details: 1832 MEANINGFUL PROTON-PROTON DISTANCE RESTRAINTS, 103 DIHEDRAL ANGLES RESTRAINTS AND 28 PROTON PAIRS STEREOSPECIFICALLY ASSIGNED WERE USED FOR STRUCTURE CALCULATIONS OF THE MONOMER. INTRA- ...Details: 1832 MEANINGFUL PROTON-PROTON DISTANCE RESTRAINTS, 103 DIHEDRAL ANGLES RESTRAINTS AND 28 PROTON PAIRS STEREOSPECIFICALLY ASSIGNED WERE USED FOR STRUCTURE CALCULATIONS OF THE MONOMER. INTRA-SUBUNIT NOES, DIHEDRAL ANGLE RESTRAINTS AND PROTON PAIRS STEREOSPECIFICALLY ASSIGNED WERE THEN DUPLICATED FOR EACH SUBUNIT IN THE STRUCTURE CALCULATIONS OF THE DIMER
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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