6K6W | pdb_00006k6w

Structure of RNase J2 from Staphylococcus epidermidis

PDB DOI: https://doi.org/10.2210/pdb6K6W/pdb

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

Deposited: 2019-06-05 Released: 2020-10-07
Deposition Author(s): Raj, R., Gopal, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.255 (Depositor), 0.254 (DCC)
R-Value Work:
0.200 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (Depositor)

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This is version 1.1 of the entry. See complete history.

Literature

Structure of RNase J1 from Staphylococcus epidermidis

Raj, R., Gopal, B.

(2020) J Biological Chem

Macromolecule Content

Total Structure Weight: 257.74 kDa
Atom Count: 13,403
Modeled Residue Count: 1,772
Deposited Residue Count: 2,284
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J 2	A, B, C, D	571	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0 Gene Names: rnj2 EC: 3.1
UniProt
Find proteins for Q8CST0 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CST0 Go to UniProtKB: Q8CST0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8CST0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.255 (Depositor), 0.254 (DCC)
R-Value Work: 0.200 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.55	α = 90
b = 131.04	β = 91.72
c = 115.9	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-10-07
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.