8SBF | pdb_00008sbf

Full-length structure of the LysR-type transcriptional regulator, ACIAD0746, from Acinetobacter baylyi

PDB DOI: https://doi.org/10.2210/pdb8SBF/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-03 Released: 2024-04-17
Deposition Author(s): Momany, C., Nune, M., Brondani, J.C., Afful, D., Neidle, E., Galloway, N.R.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8SBF

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

Literature

FinR, a LysR-type transcriptional regulator involved in sulfur homeostasis with homologs in diverse microorganisms

Momany, C., Nune, M., Brondani, J.C., Afful, D., Neidle, E., Galloway, N.R.

To be published.

Macromolecule Content

Total Structure Weight: 134.36 kDa
Atom Count: 9,823
Modeled Residue Count: 1,177
Deposited Residue Count: 1,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator (LysR family)	A, B [auth C], C [auth B], D	300	Acinetobacter baylyi ADP1	Mutation(s): 0 Gene Names: ACIAD0746
UniProt
Find proteins for Q6FE56 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore Q6FE56 Go to UniProtKB: Q6FE56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6FE56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth C], G [auth C], L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain L [auth B] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain N [auth B]	E [auth A], H [auth C], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.597	α = 90
b = 109.69	β = 90
c = 110.268	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1024108

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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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.