6IZK | pdb_00006izk

Structural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb6IZK/pdb

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


• Deposited: 2018-12-19 Released: 2020-01-22 
• Deposition Author(s): Sangare, L., Chen, W., Wang, C., Chen, X., Wu, M., Zhang, X., Zang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of mutated NreA protein in nitrate binding site from Staphylococcus aureus

Sangare, L., Cheng, W.

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: 34.52 kDa 
• Atom Count: 2,355 
• Modeled Residue Count: 284 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NreA	A, B	150	Staphylococcus aureus	Mutation(s): 1  Gene Names: QU38_07700
UniProt
Find proteins for Q2FVM5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FVM5  Go to UniProtKB:  Q2FVM5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
IMD	D [auth A], E [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	F [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.072	α = 90
b = 38.782	β = 91.57
c = 70.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Sangare, L., Chen, W., Wang, C., Chen, X., Wu, M., Zhang, X., Zang, J.

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description