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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(PAPAPAPAP*A)-3')	C, D	5	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

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

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Entry History

Deposition Data

Released Date: 2017-01-04

Deposition Author(s):

Li, D.F.

Feng, N.

Revision History (Full details and data files)

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