1RYK | pdb_00001ryk

Solution NMR Structure Protein yjbJ from Escherichia coli. Northeast Structural Genomics Consortium Target ET93; Ontario Centre for Structural Proteomics target EC0298_1_69;

• PDB DOI: https://doi.org/10.2210/pdb1RYK/pdb
• Entry: 1RYK supersedes: 1JYG
• BMRB: 5105

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


• Deposited: 2003-12-22 Released: 2004-02-24 
• Deposition Author(s): Pineda-Lucena, A., Liao, J., Wu, B., Yee, A., Cort, J.R., Kennedy, M.A., Edwards, A.M., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

An NMR approach to structural proteomics.

Pineda-Lucena, A., Liao, J., Wu, B., Yee, A., Cort, J.R., Kennedy, M.A., Edwards, A.M., Arrowsmith, C.H.

(2002) Proteins 47: 572-574

• PubMed: 11854485 
• DOI: https://doi.org/10.1073/pnas.042684599
• Primary Citation Related Structures: 
  1JCU, 1JDQ, 1JE3, 1JRM, 1JW2, 1JW3, 1RYJ, 1RYK


• PubMed Abstract: 
  

  The influx of genomic sequence information has led to the concept of structural proteomics, the determination of protein structures on a genome-wide scale. Here we describe an approach to structural proteomics of small proteins using NMR spectroscopy. Over 500 small proteins from several organisms were cloned, expressed, purified, and evaluated by NMR. Although there was variability among proteomes, overall 20% of these proteins were found to be readily amenable to NMR structure determination. NMR sample preparation was centralized in one facility, and a distributive approach was used for NMR data collection and analysis. Twelve structures are reported here as part of this approach, which allowed us to infer putative functions for several conserved hypothetical proteins.

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Organizational Affiliation: 
• Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada M5G 1L7.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.34 kDa 
• Atom Count: 587 
• Modeled Residue Count: 69 
• Deposited Residue Count: 69 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein yjbJ	A	69	Escherichia coli	Mutation(s): 0  Gene Names: YJBJ, B4045, Z5644, ECS5028, SF4160, S3571
UniProt
Find proteins for P68206 (Escherichia coli (strain K12)) Explore P68206  Go to UniProtKB:  P68206

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Pineda-Lucena, A., Liao, J., Wu, B., Yee, A., Cort, J.R., Kennedy, M.A., Edwards, A.M., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)
• This entry supersedes: 1JYG

Revision History  

• Version 1.0: 2004-02-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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
• Version 1.4: 2024-05-22
  Changes: Data collection