7MMQ | pdb_00007mmq

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Reduced Hydroquinone Form

• PDB DOI: https://doi.org/10.2210/pdb7MMQ/pdb

• Classification: Oxidoreductase/FMN binding Protein
• Organism(s): Aerococcus sp. Group 1, Aerococcus urinae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-30 Released: 2022-05-04 
• Deposition Author(s): Palowitch, G.M., Boal, A.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Ribonucleotide Reductase

Palowitch, G.M., Boal, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 225.33 kDa 
• Atom Count: 14,639 
• Modeled Residue Count: 1,759 
• Deposited Residue Count: 1,956 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase	A, B, C, D	342	Aerococcus sp. Group 1	Mutation(s): 0  Gene Names: HMPREF9243_0731 EC: 1.17.4.1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NrdI	E, F [auth G], G [auth F], H	147	Aerococcus urinae	Mutation(s): 0  Gene Names: nrdI, CYJ29_07405, DBT54_07500
UniProt
Find proteins for A0A178HGH7 (Aerococcus urinae) Explore A0A178HGH7  Go to UniProtKB:  A0A178HGH7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	L [auth E], M [auth G], N [auth F], O [auth H]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	I [auth B], J [auth C], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.385	α = 90
b = 105.012	β = 100.58
c = 138.128	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Palowitch, G.M., Boal, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description