4P1L

Crystal structure of a trap periplasmic solute binding protein from chromohalobacter salexigens dsm 3043 (csal_2479), target EFI-510085, with bound d-glucuronate, spg i213

• PDB DOI: https://doi.org/10.2210/pdb4P1L/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Chromohalobacter salexigens DSM 3043
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2014-03-19 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

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: 74.95 kDa 
• Atom Count: 5,412 
• Modelled Residue Count: 603 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP dicarboxylate transporter, DctP subunit	A, B	326	Chromohalobacter salexigens DSM 3043	Mutation(s): 0  Gene Names: Csal_2479
UniProt
Find proteins for Q1QUN2 (Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QUN2  Go to UniProtKB:  Q1QUN2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDP	C [auth A], F [auth B]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N
SO4	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.12	α = 90
b = 158.12	β = 90
c = 158.12	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Structure summary
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2015-02-25
  Changes: Database references
• Version 1.4: 2017-09-20
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.7: 2023-12-27
  Changes: Data collection, Database references, Structure summary