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- PDB-2jxi: Solution structure of the DNA-binding domain of Pseudomonas putid... -

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Basic information

Entry
Database: PDB / ID: 2jxi
TitleSolution structure of the DNA-binding domain of Pseudomonas putida Proline utilization A (putA) bound to GTTGCA DNA sequence
Components
  • DNA (5'-D(*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DC)-3')
  • DNA (5'-D(*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DT)-3')
  • Proline dehydrogenase
KeywordsDNA BINDING PROTEIN / DNA / PutA / Proline / Utilization
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / proline biosynthetic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like ...: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / Arc Repressor Mutant / FAD-linked oxidoreductase-like / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Bifunctional protein PutA / Bifunctional protein PutA
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHalouska, S. / Zhou, Y. / Becker, D. / Powers, R.
CitationJournal: Proteins / Year: 2008
Title: Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex
Authors: Halouska, S. / Zhou, Y. / Becker, D.F. / Powers, R.
History
DepositionNov 19, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 27, 2015Group: Source and taxonomy
Revision 1.3May 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline dehydrogenase
B: Proline dehydrogenase
C: DNA (5'-D(*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DT)-3')
D: DNA (5'-D(*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)18,9464
Polymers18,9464
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)1 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Proline dehydrogenase /


Mass: 5191.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q9R9T7, UniProt: Q88D80*PLUS
#2: DNA chain DNA (5'-D(*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DT)-3')


Mass: 4262.764 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DC)-3')


Mass: 4298.819 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 82 uM [U-100% 13C; U-100% 15N] PutA45, 82 uM DNA, 200 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
82 uMPutA45[U-100% 13C; U-100% 15N]1
82 uMDNA1
200 mMsodium chloride1
Sample conditionsIonic strength: 200mM NaCl / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvinrefinement
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: 100 / Conformers submitted total number: 1

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