+Open data
-Basic information
Entry | Database: PDB / ID: 6bi6 | ||||||
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Title | Solution NMR structure of uncharacterized protein YejG | ||||||
Components | Uncharacterized protein YejG | ||||||
Keywords | UNKNOWN FUNCTION / PF13989 / YejG | ||||||
Function / homology | Uncharacterised protein family YejG / YejG-like protein / Uncharacterized protein YejG Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / molecular dynamics simulation, energy refinement | ||||||
Authors | Mohanty, B. / Finn, T.J. / Macindoe, I. / Zhong, J. / Patrick, W.M. / Mackay, J.P. | ||||||
Citation | Journal: Proteins / Year: 2019 Title: The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G. Authors: Mohanty, B. / Hanson-Manful, P. / Finn, T.J. / Chambers, C.R. / McKellar, J.L.O. / Macindoe, I. / Helder, S. / Setiyaputra, S. / Zhong, Y. / Mackay, J.P. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bi6.cif.gz | 580.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bi6.ent.gz | 490.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/6bi6 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bi6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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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: 12557.149 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yejG, b2181, JW2169 / Plasmid: pGEX-6p Details (production host): For production of GST-tagged YejG Production host: Escherichia coli (E. coli) / References: UniProt: P0AD21 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 600 uM [U-13C,15N] YejG, 20 mM Bi-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 90% H2O/10% D2O Details: 600 uM [U-13C,15N]-labelled YejG 20 mM Bis-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 10% D2O; pH 6.5 Label: [U-13C,15N]-labelled YejG / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics simulation, energy refinement / Software ordinal: 7 Details: Koradi, R., Billeter, M. and Guntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation | |||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with lowest energy and acceptable covalent geometry Conformers calculated total number: 40 / Conformers submitted total number: 15 |