5XGF | pdb_00005xgf

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 Å
R-Value Free:
0.256 (Depositor), 0.259 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5XGF

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
Modeled Residue Count: 271
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Å
R-Value Free: 0.256 (Depositor), 0.259 (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 ( Å )	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

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View more in-depth experimental data

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

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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.