4TRD

Crystal structure of Staphylcoccal nuclease variant Delta+PHS I72K/V74K at pH 9.0 at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb4TRD/pdb

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


• Deposited: 2014-06-16 Released: 2014-07-16 
• Deposition Author(s): Sorenson, J.L., 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: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Crystal structure of Staphylcoccal nuclease variant Delta+PHS I72K/V74K at pH 9.0 at cryogenic temperature

Sorenson, J.L., 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: 16.63 kDa 
• Atom Count: 1,297 
• Modelled Residue Count: 131 
• 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

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: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.809	α = 90
b = 60.204	β = 90
c = 73.827	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Sorenson, J.L., 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	NIH-GM061597

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2015-02-25
  Changes: Derived calculations
• Version 1.3: 2017-09-06
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence, Database references
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description