6ETB | pdb_00006etb

Aerobic S262Y mutation of E. coli FLRD core

PDB DOI: https://doi.org/10.2210/pdb6ETB/pdb

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

Deposited: 2017-10-26 Released: 2018-11-07
Deposition Author(s): Borges, P.T., Romao, C.V., Carrondo, M.A., Teixeira, M., Frazao, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.200 (Depositor), 0.268 (DCC)
R-Value Work:
0.200 (Depositor), 0.257 (DCC)
R-Value Observed:
0.200 (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

A tyrosine mutation in E. coli flavodiiron protein increases radiation sensitivity in the crystal structure

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

To be published.

Macromolecule Content

Total Structure Weight: 95.44 kDa
Atom Count: 7,339
Modeled Residue Count: 800
Deposited Residue Count: 824
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	412	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 Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	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 D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	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 F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-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]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.200 (Depositor), 0.268 (DCC)
R-Value Work: 0.200 (Depositor), 0.257 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.383	α = 90
b = 64.407	β = 91.09
c = 147.254	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-07
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

6ETB | pdb_00006etb

Aerobic S262Y mutation of E. coli FLRD core

Literature

A tyrosine mutation in E. coli flavodiiron protein increases radiation sensitivity in the crystal structure

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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