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Yorodumi- PDB-1vee: NMR structure of the hypothetical rhodanese domain At4g01050 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vee | ||||||
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Title | NMR structure of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana | ||||||
Components | proline-rich protein family | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / rhodanese domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane protein complex / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. ...Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. #1: Journal: J.Biomol.NMR / Year: 2004 Title: NMR Assignment of the Hypothetical Rhodanese Domain At4g01050 from Arabidopsis Thaliana Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, ...Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / 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 | 1vee.cif.gz | 770.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vee.ent.gz | 646.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vee_validation.pdf.gz | 353.8 KB | Display | wwPDB validaton report |
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Full document | 1vee_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 1vee_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 1vee_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1vee ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1vee | HTTPS FTP |
-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: 14201.863 Da / Num. of mol.: 1 / Fragment: RHODANESE 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 RAFL06-68-J04 / Plasmid: P030120-27 / References: UniProt: Q9M158 |
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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: 1.1mM 13C, 15N-arabidopsis rhodanese hypothetical domain; 20mM Phosphate buffer; 100mM NA 1mM dithiothreitol; 0.02% NA3N; 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: NULL / pH: 7 / 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 |