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Yorodumi- PDB-1vdy: NMR Structure of the hypothetical ENTH-VHS domain At3g16270 from ... -
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-Basic information
Entry | Database: PDB / ID: 1vdy | ||||||
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Title | NMR Structure of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana | ||||||
Components | hypothetical protein (RAFL09-17-B18)Hypothesis | ||||||
Keywords | structural genomics / unknown function / Hypothetical protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information clathrin-coated vesicle cargo loading / clathrin-coated vesicle / clathrin binding / phosphatidylinositol binding / ubiquitin binding / trans-Golgi network / endosome Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. ...Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the hypothetical ENTH-VHS domain AT3G16270 from arabidopsis thaliana Authors: Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / ...Authors: Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. #1: Journal: J.Biomol.NMR / Year: 2004 Title: NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana Authors: Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / ...Authors: Lopez-Mendez, B. / Pantoja-Uceda, D. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vdy.cif.gz | 842.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vdy.ent.gz | 708.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vdy ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vdy | 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: 15583.571 Da / Num. of mol.: 1 / Fragment: ENTH-VHS hypothetical domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: E.Coli Cell-free protein synthesis / Gene: RIKEN CDNA RAFL09-17-B18 / Plasmid: P021216-68 / References: UniProt: Q9C5H4 |
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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: 1.20mM 13C, 15N-Arabidopsis ENTH-VHS hypothetical domain; 20mM Tris buffer; 100mM NaCl; 1mM dithiothreitol; 0.02% Na3N; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 7.5 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |