9DSY

Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid

• PDB DOI: https://doi.org/10.2210/pdb9DSY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-09-30 Released: 2024-10-09 
• Deposition Author(s): Minasov, G., Shukla, S., Shuvalova, L., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.189 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid

Minasov, G., Shukla, S., Shuvalova, L., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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 Evidence: homology

Macromolecule Content

• Total Structure Weight: 35.87 kDa 
• Atom Count: 2,897 
• Modelled Residue Count: 303 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4-dicarboxylate-binding periplasmic protein DctP	A	311	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: dctP, PA5167
UniProt
Find proteins for Q9HU18 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HU18  Go to UniProtKB:  Q9HU18

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.35 Å
• R-Value Free: 0.189 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.585	α = 78.78
b = 44.495	β = 84.22
c = 47.239	γ = 75.83

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Minasov, G., Shukla, S., Shuvalova, L., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release