3HZX

Crystal Structure of Staphylococcal nuclease variant D+PHS/V66K at pH 9 determined at 100 K

• PDB DOI: https://doi.org/10.2210/pdb3HZX/pdb

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


• Deposited: 2009-06-24 Released: 2010-05-19 
• Deposition Author(s): Schlessman, J.L., De Luca-Westrate, J.N., Garcia-Moreno, B.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Structure of Staphylococcal nuclease D+PHS/V66K reveals internal hydration in protein cavity

Harms, M.J., Schlessman, J.L., De Luca-Westrate, J.N., Garcia-Moreno, B.E.

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: 16.62 kDa 
• Atom Count: 1,161 
• Modelled Residue Count: 129 
• 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): 6  Gene Names: nuc EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THP	C [auth A]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.051	α = 90
b = 60.439	β = 94.61
c = 37.459	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Schlessman, J.L., De Luca-Westrate, J.N., Garcia-Moreno, B.E.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description