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- PDB-2asy: Solution Structure of ydhR protein from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2asy
TitleSolution Structure of ydhR protein from Escherichia coli
ComponentsProtein ydhR precursor
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / dimeric apha+beta barrel / homodimer / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function
Putative monooxygenase YdhR / Putative mono-oxygenase ydhR / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative monooxygenase YdhR / Putative monooxygenase YdhR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing,torsion angle dynamics, molecular dynamics, refinement in presence of solvent
AuthorsRevington, M. / Semesi, A. / Yee, A. / Shaw, G.S. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of the Escherichia coli protein ydhR: A putative mono-oxygenase.
Authors: Revington, M. / Semesi, A. / Yee, A. / Shaw, G.S.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Protein ydhR precursor
B: Protein ydhR precursor


Theoretical massNumber of molelcules
Total (without water)27,7672
Polymers27,7672
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein ydhR precursor


Mass: 13883.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydhR / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P77225, UniProt: P0ACX3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-aliphatic region-separated NOESY
1323D 13C-aromatic region-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM U-15N,13C; 25 mM MES, 450 mM NaCl, 0.01% Sodium Azide90% H2O/10% D2O
20.5 mM U-15N,13C; 25 mM MES, 450 mM NaCl, 0.01% Sodium Azide100% D2O
Sample conditionsIonic strength: 450 mM NaCl / pH: 6.5 / Pressure: Ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Inc.collection
NMRPipe2.3Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
NMRView5.2.2Bruce Johnsondata analysis
CYANA2.032.3untert, P., Mumenthaler, C. and Wuthrich, K.refinement
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
RefinementMethod: simulated annealing,torsion angle dynamics, molecular dynamics, refinement in presence of solvent
Software ordinal: 1
Details: 3461 NOE distance constraints 200 dihedral angle constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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