5DKV

Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose

• PDB DOI: https://doi.org/10.2210/pdb5DKV/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Allorhizobium ampelinum S4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-04 Released: 2015-09-30 
• Deposition Author(s): Yadava, U., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.171 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose

Yadava, U., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.67 kDa 
• Atom Count: 10,665 
• Modelled Residue Count: 1,199 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate binding protein (Ribose)	A, B, C, D	324	Allorhizobium ampelinum S4	Mutation(s): 0  Gene Names: rbsB, Avi_5339
UniProt
Find proteins for B9K0T2 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9K0T2  Go to UniProtKB:  B9K0T2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T6T	E [auth A], F [auth B], G [auth C], H [auth D]	alpha-D-tagatopyranose C6 H12 O6 LKDRXBCSQODPBY-VANKVMQKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.171 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.181	α = 87.41
b = 65.887	β = 90.26
c = 79.66	γ = 82.23

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Yadava, U., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 2.0: 2017-11-15
  Changes: Advisory, Atomic model, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary