9CIK | pdb_00009cik

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb9CIK/pdb

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


• Deposited: 2024-07-03 Released: 2024-08-07 
• Deposition Author(s): Zhang, Y., Schlessman, J.L., SIegler, M.A., Garcia-Moreno E., B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature

Zhang, Y., Schlessman, J.L., Robinson, A.C., Garcia-Moreno E., B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.65 kDa 
• Atom Count: 1,184 
• Modeled 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): 2  Gene Names: nuc, SACOL0860 EC: 3.1.31.1
UniProt
Find proteins for Q5HHM4 (Staphylococcus aureus (strain COL)) Explore Q5HHM4  Go to UniProtKB:  Q5HHM4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.875	α = 90
b = 60.382	β = 94.06
c = 38.196	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Zhang, Y., Schlessman, J.L., SIegler, M.A., Garcia-Moreno E., B.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 061597

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release