4MN5 | pdb_00004mn5

Crystal structure of PAS domain of S. aureus YycG

• PDB DOI: https://doi.org/10.2210/pdb4MN5/pdb

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


• Deposited: 2013-09-10 Released: 2014-09-10 
• Deposition Author(s): Shaikh, N., Hvorup, R., Winnen, B., Collins, B.M., King, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of PAS domain of S. aureus YycG

Shaikh, N., Hvorup, R., Winnen, B., Collins, B.M., King, G.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 1,707 
• Modeled Residue Count: 204 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein kinase WalK	A, B	128	Staphylococcus aureus	Mutation(s): 0  Gene Names: vicK, walK, yycG EC: 2.7.13.3
UniProt
Find proteins for Q9RDT3 (Staphylococcus aureus) Explore Q9RDT3  Go to UniProtKB:  Q9RDT3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 60.51	β = 90
c = 84.5	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Shaikh, N., Hvorup, R., Winnen, B., Collins, B.M., King, G.F.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary