1TH5 | pdb_00001th5

Solution structure of C-terminal domain of NifU-like protein from Oryza sativa

• PDB DOI: https://doi.org/10.2210/pdb1TH5/pdb
• BMRB: 6247

• Classification: Structural genomics, unknown function
• Organism(s): Oryza sativa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-06-01 Released: 2005-09-27 
• Deposition Author(s): Kumeta, H., Ogura, K., Asayama, M., Katoh, S., Katoh, E., Inagaki, F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

The NMR structure of the domain II of a chloroplastic NifU-like protein OsNifU1A.

Kumeta, H., Ogura, K., Asayama, M., Katoh, S., Katoh, E., Teshima, K., Inagaki, F.

(2007) J Biomol NMR 38: 161-164

• PubMed: 17431550 
• DOI: https://doi.org/10.1007/s10858-007-9155-9
• Primary Citation Related Structures: 
  1TH5


• PubMed Abstract: 
  

  NifU-like proteins are a highly conserved protein that serves as the scaffold for assembly of Fe-S clusters. Chloroplastic NifU-like proteins have tandem NifU like domains, named domain I and domain II. Although the amino acid sequences of these domains are very similar to each other, the predicted functional region for the Fe-S cluster assembly, the CXXC motif, exists only in domain I. The structure of the domain II of chloroplastic NifU-like protein OsNifU1A has an alpha-beta sandwich structure containing two alpha helices located on one side of the beta-sheet. The electrostatic surface potential of OsNifU1A domain II is predominantly positively charged. Chloroplastic NifU-like proteins are targeted to ferredoxin for transferring the Fe-S cluster. The ferredoxin presents an overall negatively charged surface, which may evoke an electrostatic association with OsNifU1A domain II.

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Organizational Affiliation: 
• Laboratory of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.11 kDa 
• Atom Count: 567 
• Modeled Residue Count: 74 
• Deposited Residue Count: 74 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NifU1	A	74	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for Q84LK7 (Oryza sativa subsp. japonica) Explore Q84LK7  Go to UniProtKB:  Q84LK7

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Kumeta, H., Ogura, K., Asayama, M., Katoh, S., Katoh, E., Inagaki, F.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection