1M35

Aminopeptidase P from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An orthorhombic form of Escherichia coli aminopeptidase P at 2.4 A resolution.

Graham, S.C.Lee, M.Freeman, H.C.Guss, J.M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 897-902

  • DOI: 10.1107/s0907444903005870
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Aminopeptidase P (AMPP) from Escherichia coli cleaves the N-terminal residue from an oligopeptide if the second residue is proline. The active site contains a dinuclear metal centre. Following earlier structural analyses of crystals in space groups P ...

    Aminopeptidase P (AMPP) from Escherichia coli cleaves the N-terminal residue from an oligopeptide if the second residue is proline. The active site contains a dinuclear metal centre. Following earlier structural analyses of crystals in space groups P6(4)22 and I4(1)22, the structure of AMPP has been solved and refined in the orthorhombic space group C222(1) at 2.4 A resolution. There are six subunits in the asymmetric unit. These are arranged in two types of tetramer. One tetramer comprises four crystallographically independent subunits, while the other comprises two pairs of subunits related by a crystallographic twofold axis. The final model of 20 994 protein atoms, 1618 water molecules and 12 metal atoms refined to residuals R = 0.195 and R(free) = 0.215. The molecular structure confirms most of the previously reported features, including the subunit-subunit interfaces in the tetramer and persistent disorder at some residues. The metal-ligand bond lengths at the active site suggest that one of the two Mn atoms is five-coordinate rather than six-coordinate.


    Related Citations: 
    • Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli
      Wilce, M.C.J., Bond, C.S., Dixon, N.E., Freeman, H.C., Guss, J.M., Lilley, P.E., Wilce, J.A.
      (1998) Proc Natl Acad Sci U S A 95: 3472

    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMINOPEPTIDASE P
A, B, C, D, E, F
440Escherichia coliMutation(s): 0 
Gene Names: pepP
EC: 3.4.11.9
Find proteins for P15034 (Escherichia coli (strain K12))
Go to UniProtKB:  P15034
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.047α = 90
b = 313.963β = 90
c = 162.034γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance