+Open data
-Basic information
Entry | Database: PDB / ID: 2asy | ||||||
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Title | Solution Structure of ydhR protein from Escherichia coli | ||||||
Components | Protein ydhR precursor | ||||||
Keywords | STRUCTURAL 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing,torsion angle dynamics, molecular dynamics, refinement in presence of solvent | ||||||
Authors | Revington, M. / Semesi, A. / Yee, A. / Shaw, G.S. / Ontario Centre for Structural Proteomics (OCSP) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2asy.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2asy.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2asy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2asy_validation.pdf.gz | 361 KB | Display | wwPDB validaton report |
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Full document | 2asy_full_validation.pdf.gz | 640.8 KB | Display | |
Data in XML | 2asy_validation.xml.gz | 70.7 KB | Display | |
Data in CIF | 2asy_validation.cif.gz | 107.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2asy ftp://data.pdbj.org/pub/pdb/validation_reports/as/2asy | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 450 mM NaCl / pH: 6.5 / Pressure: Ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |