7R2O | pdb_00007r2o

Crystal structure of a flavodiiron protein S262Y mutant in the oxidized state from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb7R2O/pdb

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

Deposited: 2022-02-05 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: 1.85 Å
R-Value Free:
0.184 (Depositor), 0.189 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7R2O

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a flavodiiron protein S262Y 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: 110 kDa
Atom Count: 7,109
Modeled Residue Count: 802
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 3 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 F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
FEO Query on FEO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MU-OXO-DIIRON Fe₂ O NPMYUMBHPJGBFA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.184 (Depositor), 0.189 (DCC)
R-Value Work: 0.184 (Depositor), 0.184 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.968	α = 90
b = 64.019	β = 120.42
c = 88.882	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.