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Yorodumi- PDB-2dcp: Fully automated NMR structure determination of the ENTH-VHS domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dcp | ||||||
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Title | Fully automated NMR structure determination of the ENTH-VHS domain AT3G16270 from Arabidopsis thaliana | ||||||
Components | hypothetical protein (RAFL09-17-B18) | ||||||
Keywords | UNKNOWN FUNCTION / Fully automated structure determination / FLYA algorithm | ||||||
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 / Fully automated NMR spectrum analysis, structure calculation without human intervention. Chemical shift assignments, conformational restraints have not been verified manually. | ||||||
Authors | Lopez-Mendez, B. / Guntert, P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2006 Title: Automated Protein Structure Determination from NMR Spectra Authors: Lopez-Mendez, B. / 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 | 2dcp.cif.gz | 843.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dcp.ent.gz | 709.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dcp_validation.pdf.gz | 355.5 KB | Display | wwPDB validaton report |
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Full document | 2dcp_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 2dcp_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 2dcp_validation.cif.gz | 67.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/2dcp ftp://data.pdbj.org/pub/pdb/validation_reports/dc/2dcp | HTTPS FTP |
-Related structure data
-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 domain At3g16270 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 / Production host: Cell free synthesis / 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 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 | Ionic strength: 100mM / 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: Fully automated NMR spectrum analysis, structure calculation without human intervention. Chemical shift assignments, conformational restraints have not been verified manually. 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 |