Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 40.18 kDa 
• Atom Count: 3677 
• Modelled Residue Count: 355 
• Deposited Residue Count: 361 
• Unique protein chains: 1

3OYV

Crystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus ATCC 8483 at 1.25 A resolution

• PDB DOI: 10.2210/pdb3OYV/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-23 Released: 2010-10-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

Xu, Q., Rawlings, N.D., Farr, C.L., Chiu, H.J., Grant, J.C., Jaroszewski, L., Klock, H.E., Knuth, M.W., Miller, M.D., Weekes, D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2011) PLoS One 6: e21875-e21875

• PubMed: 21799754 
• DOI: 10.1371/journal.pone.0021875
• Primary Citation of Related Structures:  
  3N8U, 3OYV


• PubMed Abstract: 
  

Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution), have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.

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Organizational Affiliation: 

Joint Center for Structural Genomics, La Jolla, California, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imelysin	A	361	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_03801
UniProt
Find proteins for A7M120 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153)) Explore A7M120  Go to UniProtKB:  A7M120

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	B [auth A]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.163 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: C 1 2 1
• Diffraction Data DOI: 10.18430/M33OYV Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.427	α = 90
b = 47.921	β = 124.62
c = 83.914	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-23 
• Released Date: 2010-10-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2011-08-10
  Changes: Database references
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence