2XPH

Crystal structure of human SENP1 with the bound cobalt

• PDB DOI: https://doi.org/10.2210/pdb2XPH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-26 Released: 2010-09-08 
• Deposition Author(s): Rimsa, V., Eadsforth, T., Hay, R.T., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.313 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 

Literature

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

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

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 442

• PubMed: 21505236 
• DOI: https://doi.org/10.1107/S1744309111005835
• Primary Citation of Related Structures:  
  2XPH, 2XRE


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.77 kDa 
• Atom Count: 3,978 
• Modelled Residue Count: 453 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENTRIN-SPECIFIC PROTEASE 1	A, B	238	Homo sapiens	Mutation(s): 0  EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U3 (Homo sapiens) Explore Q9P0U3  Go to UniProtKB:  Q9P0U3
PHAROS:  Q9P0U3 GTEx:  ENSG00000079387

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	I [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.313 
• R-Value Work: 0.227 
• R-Value Observed: 0.231 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.172	α = 90
b = 71.172	β = 90
c = 199.988	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Rimsa, V., Eadsforth, T., Hay, R.T., Hunter, W.N.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references, Non-polymer description, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description