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 

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