9C11 | pdb_00009c11

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36R at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb9C11/pdb

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


• Deposited: 2024-05-28 Released: 2024-06-19 
• Deposition Author(s): Zhang, Y., Schlessman, J.L., Siegler, M.A., Garcia-Moreno E., B.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Domain-swapping promoted by the introduction of a charge in the hydrophobic interior of a protein

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 33.22 kDa 
• Atom Count: 2,413 
• Modeled Residue Count: 271 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease A	A, B	143	Staphylococcus aureus	Mutation(s): 4  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], D [auth B]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.183	α = 90
b = 53.201	β = 90
c = 107.422	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: 2024-06-19 
Deposition Author(s): Zhang, Y., Schlessman, J.L., Siegler, M.A., Garcia-Moreno E., B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1517378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 061597

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release