4WOR | pdb_00004wor

Staphylococcal nuclease in complex with Ca2+ and thymidine-3'-5'-diphosphate (pdTp) at room temperature

• PDB DOI: https://doi.org/10.2210/pdb4WOR/pdb

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


• Deposited: 2014-10-16 Released: 2014-10-29 
• Deposition Author(s): Wall, M.E., Ealick, S.E., Gruner, S.M.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease.

Wall, M.E., Ealick, S.E., Gruner, S.M.

(1997) Proc Natl Acad Sci U S A : 6180-6184

• PubMed: 9177191 
• DOI: https://doi.org/10.1073/pnas.94.12.6180
• Primary Citation Related Structures: 
  4WOR


• PubMed Abstract: 
  

  We have developed methods for obtaining and characterizing three-dimensional maps of the reciprocal-space distribution of diffuse x-ray scattering from protein crystals, and have used the methods to study the nature of disorder in crystals of Staphylococcal nuclease. Experimentally obtained maps are 99.5% complete in the reciprocal-space resolution range of 10 A-2.5 A, show symmetry consistent with the P41 space group of the unit cell, and are highly reproducible. Quantitative comparisons of the data with three-dimensional simulations imply liquid-like motions of the protein [Caspar, D. L. D., Clarage, J., Salunke, D. M. & Clarage, M. (1988) Nature (London) 332, 659-662], with a correlation length of 10 A and a root-mean-square displacement of 0.36 A.

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Organizational Affiliation: 
• Department of Physics, Princeton University, Princeton, NJ 08544, USA.

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: 17.29 kDa 
• Atom Count: 1,142 
• Modeled Residue Count: 136 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	149	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THP	C [auth A]	THYMIDINE-3',5'-DIPHOSPHATE C10 H16 N2 O11 P2 CSNCBOPUCJOHLS-XLPZGREQSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.499	α = 90
b = 48.499	β = 90
c = 63.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Wall, M.E., Ealick, S.E., Gruner, S.M.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 2.0: 2017-09-20
  Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 2.1: 2019-12-04
  Changes: Author supporting evidence
• Version 2.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description