8Y41 | pdb_00008y41

VcFadRqm, mutant protein of Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with oleoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb8Y41/pdb

Classification: DNA
Organism(s): Vibrio cholerae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-01-30 Released: 2025-02-05
Deposition Author(s): Tsui, W., Shi, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.261 (Depositor), 0.307 (DCC)
R-Value Work:
0.248 (Depositor), 0.283 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

VcFadRqm, mutant protein of Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with oleoyl-CoA

Tsui, W., Shi, W.

To be published.

Macromolecule Content

Total Structure Weight: 66.53 kDa
Atom Count: 4,442
Modeled Residue Count: 525
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid metabolism regulator protein	A, B [auth D]	279	Vibrio cholerae	Mutation(s): 4 Gene Names: fadR, BC353_03540, D6U24_01375, ERS013165_00302, ERS013186_01100, ERS013201_00358, EYB64_05555, F0H40_07700, F0M16_02315, FLM02_10025... fadR, BC353_03540, D6U24_01375, ERS013165_00302, ERS013186_01100, ERS013201_00358, EYB64_05555, F0H40_07700, F0M16_02315, FLM02_10025, FLM12_09940, I7465_02975
UniProt
Find proteins for Q9KQU8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQU8 Go to UniProtKB: Q9KQU8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KQU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3VV (Subject of Investigation/LOI) Query on 3VV Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain C [auth A] MOL2 format, chain F [auth D] MOL2 format, chain C [auth A] mmCIF format, chain F [auth D] mmCIF format, chain C [auth A]	C [auth A], F [auth D]	S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) C₃₉ H₆₈ N₇ O₁₇ P₃ S XDUHQPOXLUAVEE-BPMMELMSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth D] Interactions & Density Focus chain C [auth A] Focus chain F [auth D]
CD (Subject of Investigation/LOI) Query on CD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth D] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth D], H [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth D] Focus chain H [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth D] Focus chain H [auth D]