5XGF

The fatty acid-responsive FadR repressor of Vibrio alginolyticus

PDB DOI: https://doi.org/10.2210/pdb5XGF/pdb
Entry: 5XGF supersedes: 5DV1

Classification: TRANSCRIPTION
Organism(s): Vibrio diabolicus E0666
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-13 Released: 2017-05-31
Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 ?
R-Value Free:
0.256 (Depositor), 0.260 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing

Feng, Y.J., Lin, Y., Li, D.F., Zhang, H.M., Gao, R.S., Bi, L.J., Wang, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 34.46 kDa
Atom Count: 2,312
Modelled Residue Count: 271
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid metabolism regulator protein	A	300	Vibrio diabolicus E0666	Mutation(s): 0
UniProt
Find proteins for A0A0H0Y8X2 (Vibrio alginolyticus) Explore A0A0H0Y8X2 Go to UniProtKB: A0A0H0Y8X2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H0Y8X2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 ?
R-Value Free: 0.256 (Depositor), 0.260 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 76	α = 90
b = 76	β = 90
c = 144.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

This entry supersedes: 5DV1

Revision History (Full details and data files)

Version 1.0: 2017-05-31
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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.