2XRE

Detection of cobalt in previously unassigned human SENP1 structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Role of Co2+ in the Crystallization of Human Senp1 and Comments on the Limitations of Automated Refinement Protocols

Rimsa, V.Eadsforth, T.Hunter, W.N.

(2011) Acta Crystallogr.,Sect.F 67: 442

  • DOI: 10.1107/S1744309111005835
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium-resolution electron-density map of the catalytic domain of human sentrin-specific protease 1 (SENP1), a strong fe ...

    Metal ions often stabilize intermolecular contacts between macromolecules, thereby promoting crystallization. When interpreting a medium-resolution electron-density map of the catalytic domain of human sentrin-specific protease 1 (SENP1), a strong feature indicative of an ordered divalent cation was noted. This was assigned as Co(2+), an essential component of the crystallization mixture. The ion displays tetrahedral coordination by Glu430 and His640 from one molecule and the corresponding residues from a symmetry-related molecule. Analysis of the data derived from a previous structure of SENP1 suggested that Co(2+) had been overlooked and re-refinement supported this conclusion. High-throughput automated re-refinement protocols also failed to mark the Co(2+) position, supporting the requirement for the incorporation of as much information as possible to enhance the value of such protocols.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SENTRIN-SPECIFIC PROTEASE 1
A, B
230Homo sapiensMutation(s): 0 
Gene Names: SENP1
EC: 3.4.22.-
Find proteins for Q9P0U3 (Homo sapiens)
Go to Gene View: SENP1
Go to UniProtKB:  Q9P0U3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.981α = 90.00
b = 71.981β = 90.00
c = 200.640γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2012-10-03
    Type: Derived calculations
  • Version 1.3: 2013-11-20
    Type: Derived calculations, Source and taxonomy
  • Version 1.4: 2019-05-29
    Type: Data collection, Experimental preparation, Other