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Yorodumi- PDB-7ccn: The binding structure of a lanthanide binding tag (LBT3) with lut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ccn | ||||||
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Title | The binding structure of a lanthanide binding tag (LBT3) with lutetium ion (Lu3+) | ||||||
Components | LBT3 | ||||||
Keywords | DE NOVO PROTEIN / Lanthanide-Binding Peptide Lanthanum ion | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Hatanaka, T. / Kikkawa, N. / Matsugami, A. / Hosokawa, Y. / Hayashi, F. / Ishida, N. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: The origins of binding specificity of a lanthanide ion binding peptide. Authors: Hatanaka, T. / Kikkawa, N. / Matsugami, A. / Hosokawa, Y. / Hayashi, F. / Ishida, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ccn.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ccn.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ccn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ccn_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 7ccn_full_validation.pdf.gz | 599.1 KB | Display | |
Data in XML | 7ccn_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 7ccn_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/7ccn ftp://data.pdbj.org/pub/pdb/validation_reports/cc/7ccn | HTTPS FTP |
-Related structure data
Related structure data | 7ccoC C: citing same article (ref.) |
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Similar structure data | |
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/peptide | Mass: 1922.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Chemical | ChemComp-LU / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 500 uM LBT3, 30 mM [U-99% 2H] MES, 1000 uM LUTETIUM (III) ION, 90% H2O/10% D2O Label: 1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 30-100 mM / Label: 1 / pH: 6.0 / PH err: 0.1 / Pressure: ambient atm / Temperature: 283 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: medoid | |||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |