3VVZ

Crystal Strucuture of The Rhodamine 6G-Bound Form of RamR (Transcriptional Regurator of TetR Family) from Salmonella Typhimurium

PDB DOI: https://doi.org/10.2210/pdb3VVZ/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-30 Released: 2013-07-03
Deposition Author(s): Sakurai, K., Nikaido, E., Nakashima, R., Yamasaki, S., Yamaguchi, A., Nishino, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 ?
R-Value Free: 0.301
R-Value Work: 0.262
R-Value Observed: 0.264

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of multidrug-resistance regulator RamR with multiple drugs

Yamasaki, S., Nikaido, E., Nakashima, R., Sakurai, K., Fujiwara, D., Fujii, I., Nishino, K.

(2013) Nat Commun 4: 2078-2078

PubMed: 23800819 Search on PubMed
DOI: https://doi.org/10.1038/ncomms3078
Primary Citation of Related Structures:
3VVX, 3VVY, 3VVZ, 3VW0, 3VW1, 3VW2

PubMed Abstract:
RamR is a transcriptional repressor of the gene-encoding RamA protein, which controls the expression of the multidrug efflux system genes acrAB-tolC. RamR is an important multidrug-resistance factor, however, its structure and the identity of the molecules to which it responds have been unknown. Here, we report the crystal structure of RamR in complex with multiple drugs, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6G. All compounds are found to interact with Phe155 of RamR, and each compound is surrounded by different amino acid residues. Binding of these compounds to RamR reduces its DNA-binding affinity, which results in the increased expression of ramA. Our results reveal significant flexibility in the substrate-recognition region of RamR, which regulates the bacterial efflux participating in multidrug resistance.

Organizational Affiliation

Laboratory of Microbiology and Infectious Diseases, Division of Special Projects, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.

Macromolecule Content

Total Structure Weight: 90.34 kDa
Atom Count: 6,038
Modelled Residue Count: 736
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative regulatory protein	A, B, C, D	194	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 0 Gene Names: STM0580, STM14_0676
UniProt
Find proteins for A0A0F6AY66 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6AY66 Go to UniProtKB: A0A0F6AY66
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F6AY66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RHQ Query on RHQ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	RHODAMINE 6G C₂₈ H₃₁ N₂ O₃ IWWWBRIIGAXLCJ-KRUMMXJUSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
RHQ	PDBBind: 3VVZ	Kd: 2.64e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 ?
R-Value Free: 0.301
R-Value Work: 0.262
R-Value Observed: 0.264
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 43.717	α = 104.54
b = 54.329	β = 97.32
c = 92.296	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2013-07-24
Changes: Database references
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations