4R86

Crystal Structure of Aminoglycoside/Multidrug Efflux System AcrD from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb4R86/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-29 Released: 2014-10-08 
• Deposition Author(s): Kim, Y., Maltseva, N., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal Structure of Aminoglycoside/Multidrug Efflux System AcrD from Salmonella typhimurium

Kim, Y., Maltseva, N., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.66 kDa 
• Atom Count: 4,417 
• Modelled Residue Count: 581 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RND family aminoglycoside/multidrug efflux pump	A, B	304	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: acrD, STM2481
UniProt
Find proteins for Q8ZN77 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZN77  Go to UniProtKB:  Q8ZN77

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BR	C [auth A], E [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.224 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34r86

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.167	α = 90
b = 91.167	β = 90
c = 147.402	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Kim, Y., Maltseva, N., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary