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- PDB-2rv8: Solution Structure of the PhoP DNA-Binding Domain from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 2rv8
TitleSolution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / PhoPC / heteronuclear NOE / MTB
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesMycobacterium tuberculosis CAS/NITR204 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMacdonald, R. / Sarkar, D. / Amer, B.R. / Clubb, R.T.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis.
Authors: Macdonald, R. / Sarkar, D. / Amer, B.R. / Clubb, R.T.
History
DepositionApr 17, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)14,7241
Polymers14,7241
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)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding response regulator


Mass: 14723.726 Da / Num. of mol.: 1
Fragment: PhoPC (PhoP C-terminal domain), UNP residues 141-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CAS/NITR204 (bacteria)
Gene: J113_05350 / Production host: Escherichia coli (E. coli) / References: UniProt: R4MFJ2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D HNHA
1913D 1H-15N NOESY
11013D 1H-15N TOCSY
11113D HNCA
11223D 1H-13C NOESY aliphatic
11323D 1H-13C NOESY aromatic
11423D (H)CCH-TOCSY
11513D C(CO)NH
11623D (H)CCH-COSY
11713D HN(CA)CO
11813D 1H-13C NOESY aliphatic
11913D HBHANH
12023D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150.0 mM sodium phosphate-1, 300.0 mM sodium chloride-2, 0.01 % sodium azide-3, 1.0 mM [U-100% 13C; U-100% 15N] PhoPC-4, 93% H2O/7% D2O93% H2O/7% D2O
250.0 mM sodium phosphate-5, 300.0 mM sodium chloride-6, 0.01 % sodium azide-7, 1.0 mM [U-100% 13C; U-100% 15N] PhoPC-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50.0 mMsodium phosphate-11
300.0 mMsodium chloride-21
0.01 %sodium azide-31
1.0 mMPhoPC-4[U-100% 13C; U-100% 15N]1
50.0 mMsodium phosphate-52
300.0 mMsodium chloride-62
0.01 %sodium azide-72
1.0 mMPhoPC-8[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 350 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
TALOSCornilescu, Delaglio and Baxdihedral angle calculation
ProcheckNMRLaskowski and MacArthurstatistics
UNIOHerrmanndata analysis
UNIOHerrmannpeak picking
UNIOHerrmannstructure solution
ATNOS-CANDIDHerrmann, Guntert and Wuthrichdata analysis
ATNOS-CANDIDHerrmann, Guntert and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30 / Representative conformer: 1

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