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Yorodumi- PDB-1ny8: Solution structure of Protein yrbA from Escherichia Coli: Northea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ny8 | ||||||
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Title | Solution structure of Protein yrbA from Escherichia Coli: Northeast Structural Genomics Consortium target ER115 | ||||||
Components | Protein yrbA | ||||||
Keywords | Structural genomics / UNKNOWN FUNCTION / ER115 / YRBA / AUTOASSIGN / AUTOSTRUCTURE / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Swapna, G.V.T. / Huang, J.Y. / Acton, T.B. / Shastry, R. / Chiang, Y.-W. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution structure of Protein yrbA from Escherichia Coli: Northeast Structural Genomics Consortium target ER115 Authors: Swapna, G.V.T. / Huang, J.Y. / Acton, T.B. / Shastry, R. / Chiang, Y.-W. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ny8.cif.gz | 483.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ny8.ent.gz | 403 KB | Display | PDB format |
PDBx/mmJSON format | 1ny8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ny8_validation.pdf.gz | 341.9 KB | Display | wwPDB validaton report |
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Full document | 1ny8_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 1ny8_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 1ny8_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny8 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11119.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YRBA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: P0A9W6 |
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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. Automated resonance assignments of backbone resonances using AUTOASSIGN. Manual sidechain assignments. Automated 3D 13C-NOESY and 15N- ...Text: The Structure was determined using Triple resonance NMR. Automated resonance assignments of backbone resonances using AUTOASSIGN. Manual sidechain assignments. Automated 3D 13C-NOESY and 15N-NOESY analysis for structure determination using AUTOSTRUCTURE |
-Sample preparation
Details | Contents: 13C,15N-ER115 0.8mM in 20mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% azide Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 5.5 / Pressure: 1 atm / Temperature: 298 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: torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 1005 conformationally-restricting NOE-derived distance constraints. 74 dihedral angle restriants from Talos and 64 hydrogen-bond restraints. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest target function | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 16 |