2BA2

Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2BA2/pdb

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


• Deposited: 2005-10-13 Released: 2006-03-07 
• Deposition Author(s): Shin, D.H., Kim, J.-S., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae.

Shin, D.H., Kim, J.-S., Yokota, H., Kim, R., Kim, S.-H.

(2006) Protein Sci 15: 921-928

• PubMed: 16522803 
• DOI: https://doi.org/10.1110/ps.051993506
• Primary Citation of Related Structures:  
  2BA2


• PubMed Abstract: 
  

  We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 A resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right-handed coiled-coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled-coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled-coils. The first part, containing one stutter, is an unusual phenylalanine-rich region that is not found in any other coiled-coil structures. The second part is a highly conserved glutamine-rich region, frequently found in other trimeric coiled-coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N-terminal sequences. Based on the structural comparison with other coiled-coil structures, a probable molecular function of the DUF16 family is discussed.

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Organizational Affiliation: 

College of Pharmacy, Ewha Womans Unversity, Seoul 120-750, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.37 kDa 
• Atom Count: 2,160 
• Modelled Residue Count: 242 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical UPF0134 protein MPN010	A, B, C	85	Mycoplasmoides pneumoniae	Mutation(s): 0
UniProt
Find proteins for P75103 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75103  Go to UniProtKB:  P75103

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.559	α = 90
b = 38.874	β = 99.21
c = 68.734	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Shin, D.H., Kim, J.-S., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references