4R5Q

Crystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster

• PDB DOI: https://doi.org/10.2210/pdb4R5Q/pdb
• Entry: 4R5Q supersedes: 4ONB

• Classification: HYDROLASE
• Organism(s): Pyrobaculum calidifontis JCM 11548
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-21 Released: 2014-09-17 
• Deposition Author(s): Nocek, B., Skarina, T., Lemak, S., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Literature

Crystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster

Nocek, B., Skarina, T., Lemak, S., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.23 kDa 
• Atom Count: 1,737 
• Modelled Residue Count: 215 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated exonuclease, Cas4 family	A	216	Pyrobaculum calidifontis JCM 11548	Mutation(s): 0  Gene Names: Pcal_0546
UniProt
Find proteins for A3MTK6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1)) Explore A3MTK6  Go to UniProtKB:  A3MTK6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.253 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.836	α = 90
b = 117.836	β = 90
c = 89.412	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Nocek, B., Skarina, T., Lemak, S., Brown, G., Savchenko, A., Joachimiak, A., Yakunin, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 4ONB

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence, Refinement description