+Open data
-Basic information
Entry | Database: PDB / ID: 2lyj | ||||||
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Title | NOE-based 3D structure of the CylR2 homodimer at 298K | ||||||
Components | CylR2 | ||||||
Keywords | DNA BINDING PROTEIN / homodimer / CylR2 / NOE-based structure / protein folding / cold denaturation / cytolysin repressor 2 / helix-turn-helix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Jaremko, M. / Jaremko, L. / Kim, H. / Cho, M. / Giller, K. / Becker, S. / Zweckstetter, M. / Schwieters, C.D. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: Cold denaturation of a protein dimer monitored at atomic resolution. Authors: Jaremko, M. / Jaremko, L. / Kim, H.Y. / Cho, M.K. / Schwieters, C.D. / Giller, K. / Becker, S. / Zweckstetter, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lyj.cif.gz | 865.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lyj.ent.gz | 722.1 KB | Display | PDB format |
PDBx/mmJSON format | 2lyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lyj_validation.pdf.gz | 495.2 KB | Display | wwPDB validaton report |
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Full document | 2lyj_full_validation.pdf.gz | 803.8 KB | Display | |
Data in XML | 2lyj_validation.xml.gz | 73.4 KB | Display | |
Data in CIF | 2lyj_validation.cif.gz | 95.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/2lyj ftp://data.pdbj.org/pub/pdb/validation_reports/ly/2lyj | HTTPS FTP |
-Related structure data
Related structure data | 2lykC 2lylC 2lypC 2lyqC 2lyrC 2lysC C: citing same article (ref.) |
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Similar structure data | |
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: 7724.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: cylR2 / Plasmid: PET32A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q8VL32 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.52 mM [U-100% 13C; U-100% 15N] CylR2, strand 1, 600 mM sodium chloride, 50 mM HEPES, 93 % H2O, 7 % D2O, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.6 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |