6K6W | pdb_00006k6w

Structure of RNase J2 from Staphylococcus epidermidis

• PDB DOI: https://doi.org/10.2210/pdb6K6W/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-05 Released: 2020-10-07 
• Deposition Author(s): Raj, R., Gopal, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Structure of RNase J1 from Staphylococcus epidermidis

Raj, R., Gopal, B.

(2020) J Biological Chem 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 257.74 kDa 
• Atom Count: 13,403 
• Modeled Residue Count: 1,772 
• Deposited Residue Count: 2,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J 2	A, B, C, D	571	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0  Gene Names: rnj2 EC: 3.1
UniProt
Find proteins for Q8CST0 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CST0  Go to UniProtKB:  Q8CST0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.55	α = 90
b = 131.04	β = 91.72
c = 115.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Raj, R., Gopal, B.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references