+Open data
-Basic information
Entry | Database: PDB / ID: 2f09 | ||||||
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Title | Solution Structure of the gene product of E. coli gene ydhA | ||||||
Components | Hypothetical protein ydhA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 8 strand beta-barrel / Ontario Centre for Structural Proteomics / OCSP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics | ||||||
Authors | Shaw, G.S. / Revington, M.J. / Ontario Centre for Structural Proteomics (OCSP) | ||||||
Citation | Journal: To be Published Title: The solution structure of the Escherichia coli gene product ydhA. Authors: Shaw, G.S. / Revington, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f09.cif.gz | 560.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f09.ent.gz | 485.6 KB | Display | PDB format |
PDBx/mmJSON format | 2f09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f09_validation.pdf.gz | 350.9 KB | Display | wwPDB validaton report |
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Full document | 2f09_full_validation.pdf.gz | 486.9 KB | Display | |
Data in XML | 2f09_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 2f09_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/2f09 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/2f09 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11736.067 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ydhA / Plasmid: pEt15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28224 |
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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 | Contents: 0.5 mM ydha U-15N,U-13C, 10mM sodium phosphate, 400 mM NaCl, 10 mM dithiothreitol, 0.01% sodium azide, 1mM benzamidine, pH6.5, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 410 mM / pH: 6.5 / Pressure: ambient / Temperature: 298.0 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 Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |