3EJI

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36K at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb3EJI/pdb

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


• Deposited: 2008-09-18 Released: 2008-11-04 
• Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B., Benning, M., Isom, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.203 
• R-Value Observed: 0.209 

Literature

Structural Consequences of the Ionization of Lysines at 25 Internal Positions in a Protein

Chimenti, M.S., Khangulov, V.S., Robinson, A.C., 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: 16.37 kDa 
• Atom Count: 1,147 
• Modelled Residue Count: 130 
• 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): 5  Gene Names: nuc, SAR0847 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
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.203 
• R-Value Observed: 0.209 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.2	α = 90
b = 48.2	β = 90
c = 63.21	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B., Benning, M., Isom, D.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection