5HAA

Crystal structure of mpy-RNase J, an archaeal RNase J from Methanolobus psychrophilus R15

• PDB DOI: https://doi.org/10.2210/pdb5HAA/pdb

• Classification: HYDROLASE
• Organism(s): Methanolobus psychrophilus R15
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-30 Released: 2017-01-04 
• Deposition Author(s): Feng, N., Li, D.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.274 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

Starting Model: experimental

Literature

Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1

Zheng, X., Feng, N., Li, D.F., Li, J., Dong, X.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 105.49 kDa 
• Atom Count: 7,113 
• Modelled Residue Count: 907 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J	A, B	470	Methanolobus psychrophilus R15	Mutation(s): 0  Gene Names: rnj, Mpsy_0886 EC: 3.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.274 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.508	α = 90
b = 162.508	β = 90
c = 180.659	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-04 
Deposition Author(s): Feng, N., Li, D.F.

Revision History  

• Version 1.0: 2017-01-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description