7MMU | pdb_00007mmu

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae with Cu(I) bound (Cu acetonitrile soak)

PDB DOI: https://doi.org/10.2210/pdb7MMU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aerococcus sp. Group 1
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.195 (Depositor), 0.203 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Ribonucleotide Reductase

Palowitch, G.M., Boal, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 78.91 kDa
Atom Count: 5,242
Modeled Residue Count: 621
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase	A, B	342	Aerococcus sp. Group 1	Mutation(s): 0 Gene Names: HMPREF9243_0731 EC: 1.17.4.1
UniProt
Find proteins for A0ACD6B8K0 (Aerococcus urinae (strain CCUG 59500 / ACS-120-V-Col10a)) Explore A0ACD6B8K0 Go to UniProtKB: A0ACD6B8K0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8K0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU1 (Subject of Investigation/LOI) Query on CU1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.195 (Depositor), 0.203 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.616	α = 90
b = 46.766	β = 90.52
c = 134.077	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Palowitch, G.M.

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

Revision History (Full details and data files)

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

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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.