4F3S | pdb_00004f3s

Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica

• PDB DOI: https://doi.org/10.2210/pdb4F3S/pdb
• Entry: 4F3S supersedes: 3R39

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


• Deposited: 2012-05-09 Released: 2012-05-23 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Foti, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica

Agarwal, R., Almo, S.C., Swaminathan, S.

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)

Macromolecule Content 

• Total Structure Weight: 29.86 kDa 
• Atom Count: 1,891 
• Modeled Residue Count: 231 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative periplasmic binding protein	A	255	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: STM1633
UniProt
Find proteins for Q8ZPA3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPA3  Go to UniProtKB:  Q8ZPA3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DAL	C [auth A]	D-ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-UWTATZPHSA-N
GLY	B [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.406	α = 90
b = 80.406	β = 90
c = 187.041	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CCP4	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Foti, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)
• This entry supersedes: 3R39

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary