6K6S | pdb_00006k6s

Structure of RNase J1 from Staphylococcus epidermidis

• PDB DOI: https://doi.org/10.2210/pdb6K6S/pdb

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


• Deposited: 2019-06-04 Released: 2020-10-07 
• Deposition Author(s): Raj, R., Gopal, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.337 (Depositor), 0.360 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.320 (DCC) 
• R-Value Observed: 
  0.299 (Depositor) 

Literature

Structure of RNase J1 from Staphylococcus epidermidis

Raj, R., Gopal, B.

(2020) J Biological Chem 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 127.72 kDa 
• Atom Count: 5,837 
• Modeled Residue Count: 884 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J 1	A, B	574	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0  Gene Names: rnj1 EC: 3.1
UniProt
Find proteins for Q8CT16 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CT16  Go to UniProtKB:  Q8CT16

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.337 (Depositor), 0.360 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.320 (DCC) 
• R-Value Observed: 0.299 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.068	α = 90
b = 86.068	β = 90
c = 486.839	γ = 120

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