7MMR | pdb_00007mmr

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-NrdI complex from Aerococcus urinae in Oxidized Form with Cu(I) bound

PDB DOI: https://doi.org/10.2210/pdb7MMR/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 222.13 kDa
Atom Count: 15,225
Modeled Residue Count: 1,782
Deposited Residue Count: 1,916
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase	A, B, C, D	337	Aerococcus sp. Group 1	Mutation(s): 0 Gene Names: HMPREF9243_0731 EC: 1.17.4.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NrdI	E, F [auth G], G [auth F], H	142	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A178HGH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain FA [auth F] SDF format, chain HA [auth H] SDF format, chain BA [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth H] MOL2 format, chain BA [auth E] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth H] mmCIF format, chain BA [auth E]	BA [auth E], DA [auth G], FA [auth F], HA [auth H]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth E] Focus chain DA [auth G] Focus chain FA [auth F] Focus chain HA [auth H] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth G] Focus chain FA [auth F] Focus chain HA [auth H]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth D]	AA [auth D] K [auth A] N [auth B] O [auth B] R [auth C] AA [auth D], K [auth A], N [auth B], O [auth B], R [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain Z [auth D]
CU1 (Subject of Investigation/LOI) Query on CU1 Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] M [auth B] P [auth C] I [auth A], J [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], T [auth C], X [auth D], Y [auth D]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain IA [auth H] SDF format, chain GA [auth F] SDF format, chain EA [auth G] SDF format, chain CA [auth E] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain IA [auth H] MOL2 format, chain GA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain CA [auth E] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain IA [auth H] mmCIF format, chain GA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain CA [auth E]	CA [auth E] EA [auth G] GA [auth F] IA [auth H] U [auth C] CA [auth E], EA [auth G], GA [auth F], IA [auth H], U [auth C], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain EA [auth G] Focus chain GA [auth F] Focus chain IA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth G] Focus chain GA [auth F] Focus chain IA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]