7R0F | pdb_00007r0f

Crystal structure of a flavodiiron protein D52K mutant in the oxidized state from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb7R0F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-02-02 Released: 2023-02-15
Deposition Author(s): Borges, P.T., Teixeira, M., Romao, C.V., Frazao, C.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.205 (Depositor), 0.216 (DCC)
R-Value Work:
0.205 (Depositor), 0.230 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: other
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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

Crystal structure of a flavodiiron protein D52K mutant in the oxidized state from Escherichia coli

Borges, P.T., Teixeira, M., Romao, C.V., Frazao, C.

To be published.

Macromolecule Content

Total Structure Weight: 109.85 kDa
Atom Count: 7,053
Modeled Residue Count: 802
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaerobic nitric oxide reductase flavorubredoxin	A, B	479	Escherichia coli K-12	Mutation(s): 1 Gene Names: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680
UniProt
Find proteins for Q46877 (Escherichia coli (strain K12)) Explore Q46877 Go to UniProtKB: Q46877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]