3NJL | pdb_00003njl

D116A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis, at pH7.5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.172 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.

Osipiuk, J., Mulligan, R., Bargassa, M., Hamilton, J.E., Cunningham, M.A., Joachimiak, A.

(2012) J Biological Chem 287: 19452-19461

  • DOI: https://doi.org/10.1074/jbc.M112.358069
  • Primary Citation Related Structures: 
    3N55, 3NJF, 3NJG, 3NJH, 3NJI, 3NJJ, 3NJK, 3NJL, 3NJM, 3NJN

  • PubMed Abstract: 

    The crystal structure of SO1698 protein from Shewanella oneidensis was determined by a SAD method and refined to 1.57 Å. The structure is a β sandwich that unexpectedly consists of two polypeptides; the N-terminal fragment includes residues 1-116, and the C-terminal one includes residues 117-125. Electron density also displayed the Lys-98 side chain covalently linked to Asp-116. The putative active site residues involved in self-cleavage were identified; point mutants were produced and characterized structurally and in a biochemical assay. Numerical simulations utilizing molecular dynamics and hybrid quantum/classical calculations suggest a mechanism involving activation of a water molecule coordinated by a catalytic aspartic acid.

    • Organizational Affiliation: 
    • Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecule Content 

  • Total Structure Weight: 13.71 kDa 
  • Atom Count: 1,084 
  • Modeled Residue Count: 119 
  • Deposited Residue Count: 128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidase128Shewanella oneidensisMutation(s): 1 
Gene Names: SO_1698
UniProt
Find proteins for Q8EGA7 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EGA7 
Go to UniProtKB:  Q8EGA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EGA7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG


Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.172 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.151α = 90
b = 100.151β = 90
c = 100.216γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description