4WRD | pdb_00004wrd

Crystal structure of Staphylcoccal nulease variant Delta+PHS V66E L125E at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb4WRD/pdb

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


• Deposited: 2014-10-23 Released: 2015-07-08 
• Deposition Author(s): Bell-Upp, P.C., 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: 1.65 Å
• R-Value Free: 
  0.220 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Staphylcoccal nulease variant Delta+PHS V66E L125E at cryogenic temperature

Bell-Upp, P.C., 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: 1,203 
• Modeled Residue Count: 129 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermonuclease	A	143	Staphylococcus aureus subsp. aureus COL	Mutation(s): 6  Gene Names: nuc, SACOL0860 EC: 3.1.31.1
UniProt
Find proteins for Q5HHM4 (Staphylococcus aureus (strain COL)) Explore Q5HHM4  Go to UniProtKB:  Q5HHM4

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: 1.65 Å
• R-Value Free:  0.220 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.14	α = 90
b = 60.315	β = 94.05
c = 38.364	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Bell-Upp, P.C., 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	GM073838

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description