4N8Y

Crystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. btai1 b (bbta_0128), target EFI-510056 (bbta_0128), complex with alpha/beta-d-galacturonate

• PDB DOI: https://doi.org/10.2210/pdb4N8Y/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bradyrhizobium sp. BTAi1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-18 Released: 2013-11-20 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• 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: 72.82 kDa 
• Atom Count: 5,621 
• Modelled Residue Count: 600 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)	A, B	330	Bradyrhizobium sp. BTAi1	Mutation(s): 0  Gene Names: BBta_0128
UniProt
Find proteins for A5E8D2 (Bradyrhizobium sp. (strain BTAi1 / ATCC BAA-1182)) Explore A5E8D2  Go to UniProtKB:  A5E8D2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTR	D [auth A], F [auth B]	beta-D-galactopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-DTEWXJGMSA-N
ADA	C [auth A], E [auth B]	alpha-D-galactopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-BKBMJHBISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.175 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.798	α = 90
b = 85.705	β = 90
c = 86.246	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2015-10-14
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary