8ONO

Modified oligopeptidase B from S. proteamaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution

Petrenko, D.E.Boyko, K.M.Nikolaeva, A.Y.Vlaskina, A.V.Mikhailova, A.G.Timofeev, V.I.Rakitina, T.V.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptidase B677Serratia proteamaculansMutation(s): 0 
Gene Names: opdB
UniProt
Find proteins for B3VI58 (Serratia proteamaculans)
Explore B3VI58 
Go to UniProtKB:  B3VI58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VI58
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 100.62β = 90
c = 108.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection