5HAB | pdb_00005hab

Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA

• PDB DOI: https://doi.org/10.2210/pdb5HAB/pdb
• NAKB: 5HAB

• Classification: HYDROLASE
• Organism(s): Methanolobus psychrophilus R15, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

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: 108.29 kDa 
• Atom Count: 7,691 
• Modeled Residue Count: 929 
• Deposited Residue Count: 950 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J	A, B	470	Methanolobus psychrophilus R15	Mutation(s): 1  Gene Names: rnj, Mpsy_0886 EC: 3.1
UniProt
Find proteins for A0A6I8WFN3 (Methanolobus psychrophilus R15) Explore A0A6I8WFN3  Go to UniProtKB:  A0A6I8WFN3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*AP*A)-3')	C, D	5	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.68	α = 90
b = 169.68	β = 90
c = 167.32	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-01-04
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations