1N0E

CRYSTAL STRUCTURE OF A CELL DIVISION AND CELL WALL BIOSYNTHESIS PROTEIN UPF0040 FROM MYCOPLASMA PNEUMONIAE: INDICATION OF A NOVEL FOLD WITH A POSSIBLE NEW CONSERVED SEQUENCE MOTIF

• PDB DOI: https://doi.org/10.2210/pdb1N0E/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Mycoplasmoides pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-13 Released: 2003-10-21 
• Deposition Author(s): Chen, S., Jancrick, J., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif.

Chen, S., Jancrick, J., Yokota, H., Kim, R., Kim, S.-H.

(2004) Proteins 55: 785-791

• PubMed: 15146477 
• DOI: https://doi.org/10.1002/prot.10593
• Primary Citation of Related Structures:  
  1N0E, 1N0F, 1N0G


• PubMed Abstract: 
  

  UPF0040 is a family of proteins implicated in a cellular function of bacteria cell division. There is no structure information available on protein of this family. We have determined the crystal structure of a protein from Mycoplasma pneumoniae that belongs to this family using X-ray crystallography. Structural homology search reveals that this protein has a novel fold with no significant similarity to any proteins of known three-dimensional structure. The crystal structures of the protein in three different crystal forms reveal that the protein exists as a ring of octamer. The conserved protein residues, including a highly conserved DXXXR motif, are examined on the basis of crystal structure.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 154.74 kDa 
• Atom Count: 9,772 
• Modelled Residue Count: 1,130 
• Deposited Residue Count: 1,328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mraZ	A, B, C, D, E, F, G, H	166	Mycoplasmoides pneumoniae	Mutation(s): 0
UniProt
Find proteins for P75467 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75467  Go to UniProtKB:  P75467

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.279 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.627	α = 90
b = 100.064	β = 93.3
c = 100.851	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-21 
Deposition Author(s): Chen, S., Jancrick, J., Yokota, H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2003-10-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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