5DV5 | pdb_00005dv5

The fatty acid-responsive FadR repressor of Vibrio alginolyticus complex with Palmitoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb5DV5/pdb

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

Deposited: 2015-09-21 Released: 2016-10-05
Deposition Author(s): Lin, Y., Li, D.F., Feng, Y.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (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

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: 72.83 kDa
Atom Count: 4,675
Modeled Residue Count: 534
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GntR family transcriptional regulator	A, B	300	Vibrio alginolyticus	Mutation(s): 0 Gene Names: AAW52_18775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PKZ Query on PKZ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	Palmitoyl-CoA C₃₇ H₆₆ N₇ O₁₇ P₃ S MNBKLUUYKPBKDU-BBECNAHFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.78	α = 90
b = 88.48	β = 93.13
c = 61.65	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Lin, Y.

Li, D.F.

Feng, Y.J.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description