3D4D

Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91E at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb3D4D/pdb

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


• Deposited: 2008-05-14 Released: 2008-11-04 
• Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.233 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91E at cryogenic temperature.

Khangulov, V.S., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.1 kDa 
• Atom Count: 2,295 
• Modelled Residue Count: 258 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A, B	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	D [auth A], F [auth B]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.233 
• R-Value Observed: 0.239 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.022	α = 90
b = 81.293	β = 90.05
c = 60.385	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: 2008-11-04 
Deposition Author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B.

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description