2OF1 | pdb_00002of1

Cryogenic crystal structure of the Staphylococcal Nuclease variant truncated Delta+PHS I92W

• PDB DOI: https://doi.org/10.2210/pdb2OF1/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-01-02 Released: 2008-03-25 
• Deposition Author(s): Reynald, R.L., Gittis, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.244 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

On the presence of water molecules in the protein hydrophobic core

Reynald, R.L., Gittis, A.G.

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: 16.12 kDa 
• Atom Count: 1,241 
• Modeled Residue Count: 136 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal thermonuclease	A	138	Staphylococcus aureus	Mutation(s): 0  Gene Names: nuc EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus) Explore P00644  Go to UniProtKB:  P00644

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THP	E [auth A]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.244 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.313	α = 90
b = 63.62	β = 90
c = 46.727	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Reynald, R.L., Gittis, A.G.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description