Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.20 kDa 
• Atom Count: 1001 
• Modelled Residue Count: 134 
• Deposited Residue Count: 134 
• Unique protein chains: 1

1VEE

NMR structure of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana

• PDB DOI: 10.2210/pdb1VEE/pdb
• BMRB: 5929

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2004-03-30 Released: 2005-01-25 
• Deposition Author(s): 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)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana

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.

(2005) Protein Sci 14: 224-230

• PubMed: 15576557 
• DOI: 10.1110/ps.041138705
• Primary Citation of Related Structures:  
  1VEE


• PubMed Abstract: 
  

The three-dimensional structure of the rhodanese homology domain At4g01050(175-195) from Arabidopsis thaliana has been determined by solution nuclear magnetic resonance methods based on 3043 upper distance limits derived from NOE intensities measured in three-dimensional NOESY spectra. The structure shows a backbone root mean square deviation to the mean coordinates of 0.43 A for the structured residues 7-125. The fold consists of a central parallel beta-sheet with five strands in the order 1-5-4-2-3 and arranged in the conventional counterclockwise twist, and helices packing against each side of the beta-sheet. Comparison with the sequences of other proteins with a rhodanese homology domain in Arabidopsis thaliana indicated residues that could play an important role in the scaffold of the rhodanese homology domain. Finally, a three-dimensional structure comparison of the present noncatalytic rhodanese homology domain with the noncatalytic rhodanese domains of sulfurtransferases from other organisms discloses differences in the length and conformation of loops that could throw light on the role of the noncatalytic rhodanese domain in sulfurtransferases.

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Related Citations: 

• NMR Assignment of the Hypothetical Rhodanese Domain At4g01050 from Arabidopsis Thaliana
  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.
  (2004) J Biomol NMR 29: 207

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Organizational Affiliation: 

Tatsuo Miyazawa Memorial Program, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
proline-rich protein family	A	134	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RIKEN CDNA RAFL06-68-J04, STR4, TROL, At4g01050, F2N1.31
UniProt
Find proteins for Q9M158 (Arabidopsis thaliana) Explore Q9M158  Go to UniProtKB:  Q9M158

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 1VEE Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-30 
• Released Date: 2005-01-25 
Deposition Author(s): 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)

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations