5HAA | pdb_00005haa

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.274 (Depositor), 0.275 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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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: 105.49 kDa
Atom Count: 7,113
Modeled Residue Count: 907
Deposited Residue Count: 940
Unique protein 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): 0 Gene Names: rnj, Mpsy_0886 EC: 3.1

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.274 (Depositor), 0.275 (DCC)
R-Value Work: 0.237 (Depositor), 0.240 (DCC)
R-Value Observed: 0.240 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-01-04

Deposition Author(s):

Feng, N.

Li, D.F.

Revision History (Full details and data files)

Version 1.0: 2017-01-04
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary