8DQ3 | pdb_00008dq3

X-ray crystal structure of Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit

PDB DOI: https://doi.org/10.2210/pdb8DQ3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aggregatibacter actinomycetemcomitans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-18 Released: 2023-07-26
Deposition Author(s): Rose, H.R., Jung, J.J., Boal, A.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.195 (Depositor), 0.197 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (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

X-ray crystal structure of Aggregatibacter actinomycetemcomitans dimanganese(II) class Id ribonucleotide reductase beta subunit

Rose, H.R., Boal, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 164.52 kDa
Atom Count: 10,571
Modeled Residue Count: 1,185
Deposited Residue Count: 1,392
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase	A, B, C, D	348	Aggregatibacter actinomycetemcomitans	Mutation(s): 0 Gene Names: FXB68_03595 EC: 1.17.4.1
UniProt
Find proteins for A0A142G3G1 (Aggregatibacter actinomycetemcomitans) Explore A0A142G3G1 Go to UniProtKB: A0A142G3G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A142G3G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain H [auth A]	H [auth A], R [auth C], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain R [auth C] Focus chain V [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] J [auth B] K [auth B] O [auth C] E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], N [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], Q [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]