6EEK | pdb_00006eek

Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb6EEK/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-08-14 Released: 2018-08-29 
• Deposition Author(s): Kougentakis, C.M., Schlessman, J.L., Garcia-Moreno, E.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature

Kougentakis, C.M., Schlessman, J.L., Garcia-Moreno, E.B.

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)

Macromolecule Content 

• Total Structure Weight: 16.2 kDa 
• Atom Count: 971 
• Modeled Residue Count: 119 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	143	Staphylococcus aureus	Mutation(s): 7  Gene Names: nuc EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.309 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.795	α = 90
b = 71.795	β = 90
c = 56.804	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Kougentakis, C.M., Schlessman, J.L., Garcia-Moreno, E.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM061597

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description