4YS2 | pdb_00004ys2

RCK domain with CDA

• PDB DOI: https://doi.org/10.2210/pdb4YS2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-16 Released: 2016-04-27 
• Deposition Author(s): Chin, K.H., Chou, S.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.250 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

RCK domain with CDA

Chin, K.H., Chou, S.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.79 kDa 
• Atom Count: 1,281 
• Modeled Residue Count: 144 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na+/H+ antiporter-like protein	A, B	84	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q2FZQ4 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZQ4  Go to UniProtKB:  Q2FZQ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA	C [auth A]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C20 H24 N10 O12 P2 PDXMFTWFFKBFIN-XPWFQUROSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.250 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.195	α = 90
b = 45.843	β = 90
c = 69.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Chin, K.H., Chou, S.H.

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary