1PA4

Solution structure of a putative ribosome-binding factor from Mycoplasma pneumoniae (MPN156)

• PDB DOI: https://doi.org/10.2210/pdb1PA4/pdb
• BMRB: 5796

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Mycoplasmoides pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-13 Released: 2004-03-02 
• Deposition Author(s): Rubin, S.M., Pelton, J.G., Yokota, H., Kim, R., Wemmer, D.E., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 16 
• Selection Criteria: Submitted conformers are those with lowest DYANA target functions. 

Literature

Solution structure of a putative ribosome binding protein from Mycoplasma pneumoniae and comparison to a distant homolog.

Rubin, S.M., Pelton, J.G., Yokota, H., Kim, R., Wemmer, D.E.

(2003) J Struct Funct Genomics 4: 235-243

• PubMed: 15185964 
• DOI: https://doi.org/10.1023/b:jsfg.0000016127.57320.82
• Primary Citation of Related Structures:  
  1PA4


• PubMed Abstract: 
  

  The solution structure of MPN156, a ribosome-binding factor A (RBFA) protein family member from Mycoplasma pneumoniae, is presented. The structure, solved by nuclear magnetic resonance, has a type II KH fold typical of RNA binding proteins. Despite only approximately 20% sequence identity between MPN156 and another family member from Escherichia coli, the two proteins have high structural similarity. The comparison demonstrates that many of the conserved residues correspond to conserved elements in the structures. Compared to a structure based alignment, standard alignment methods based on sequence alone mispair a majority of amino acids in the two proteins. Implications of these discrepancies for sequence based structural modeling are discussed.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.41 kDa 
• Atom Count: 782 
• Modelled Residue Count: 96 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribosome-binding factor A	A	116	Mycoplasmoides pneumoniae	Mutation(s): 0  Gene Names: MPN156
UniProt
Find proteins for P75589 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75589  Go to UniProtKB:  P75589

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 16 
• Selection Criteria: Submitted conformers are those with lowest DYANA target functions. 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-02 
Deposition Author(s): Rubin, S.M., Pelton, J.G., Yokota, H., Kim, R., Wemmer, D.E., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-03-02
  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: 2022-02-23
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection