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- PDB-2jxh: Solution Structure of DNA binding domain of Proline Utilization A... -

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Basic information

Entry
Database: PDB / ID: 2jxh
TitleSolution Structure of DNA binding domain of Proline Utilization A (PutA) for Psuedomonas putida
ComponentsProline dehydrogenase
KeywordsDNA BINDING PROTEIN / PutA / Proline / Utilization / DNA
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / 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
Bifunctional protein PutA
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / simulated annealing
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 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline dehydrogenase
B: Proline dehydrogenase


Theoretical massNumber of molelcules
Total (without water)10,3842
Polymers10,3842
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Proline dehydrogenase


Mass: 5191.998 Da / Num. of mol.: 2 / Fragment: residues 1-45 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q9R9T7

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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 CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HNHA

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Sample preparation

DetailsContents: 2.2 mM [U-99% 13C; U-99% 15N] PutA45, 200 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.2 mMPutA45[U-99% 13C; U-99% 15N]1
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 softwareName: X-PLOR / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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