9DTL | pdb_00009dtl

Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid

PDB DOI: https://doi.org/10.2210/pdb9DTL/pdb

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

Deposited: 2024-10-01 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (DCC)
R-Value Observed:
0.173 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) 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.

Macromolecule Content

Total Structure Weight: 35.79 kDa
Atom Count: 2,839
Modeled Residue Count: 289
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4-dicarboxylate-binding periplasmic protein	A	311	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA0884
UniProt
Find proteins for Q9I561 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I561 Go to UniProtKB: Q9I561
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I561
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.195 (Depositor), 0.198 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.01	α = 90
b = 67.095	β = 90
c = 86.653	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Biology of Infectious Diseases (CSBID)

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

Revision History (Full details and data files)

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

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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.