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- PDB-2dcq: Fully automated NMR structure determination of the rhodanese homo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dcq | ||||||
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Title | Fully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana | ||||||
![]() | Putative protein At4g01050 | ||||||
![]() | UNKNOWN FUNCTION / rhodanese domain / fully automated structure determination / FLYA algorithm | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | SOLUTION NMR / Fully automated NMR spectrum analysis, structure calculation without human intervention. CHEMICAL SHIFT ASSIGNMENTS, CONFORMATIONAL RESTRAINTS HAVE NOT BEEN VERIFIED MANUALLY. | ||||||
![]() | Lopez-Mendez, B. / Guntert, P. | ||||||
![]() | ![]() Title: Automated protein structure determination from NMR spectra Authors: Lopez-Mendez, B. / Guntert, P. #1: ![]() 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. #2: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 773.2 KB | Display | ![]() |
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PDB format | ![]() | 647.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 357.5 KB | Display | ![]() |
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Full document | ![]() | 466 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 65.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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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 Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 7.0 / 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 ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |