3U9O

Crystal structure of Staphylococcal nuclease variant NVIAGA/N100G at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb3U9O/pdb

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


• Deposited: 2011-10-19 Released: 2011-11-23 
• Deposition Author(s): Schlessman, J.L., Doctrow, B.M., Garcia-Moreno E., B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.196 

Literature

Local flexibility as a determinant of pKa values of surface ionizable groups in proteins

Baran, K.L., Doctrow, B.M., Chimenti, M., Herbst, K., Fitch, C.A., Majumdar, A., 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: 16.82 kDa 
• Atom Count: 1,073 
• Modelled Residue Count: 124 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	149	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.239 
• R-Value Work: 0.191 
• R-Value Observed: 0.196 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.825	α = 90
b = 48.825	β = 90
c = 63.576	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-23 
Deposition Author(s): Schlessman, J.L., Doctrow, B.M., Garcia-Moreno E., B.

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description