5IAI

Crystal structure of ABC transporter Solute Binding Protein Arad_9887 from Agrobacterium radiobacter K84, target EFI-510945 in complex with Ribitol

• PDB DOI: https://doi.org/10.2210/pdb5IAI/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Rhizobium rhizogenes K84
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-21 Released: 2016-03-09 
• Deposition Author(s): Vetting, M.W., Bonanno, J.B., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Crystal structure of ABC transporter Solute Binding Protein Arad_9887 from Agrobacterium radiobacter K84, target EFI-510945 in complex with Ribitol

Vetting, M.W., Bonanno, J.B., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.76 kDa 
• Atom Count: 3,571 
• Modelled Residue Count: 399 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter	A	422	Rhizobium rhizogenes K84	Mutation(s): 0  Gene Names: Arad_9887
UniProt
Find proteins for B9JM84 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JM84  Go to UniProtKB:  B9JM84

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB0	B [auth A]	D-ribitol C5 H12 O5 HEBKCHPVOIAQTA-ZXFHETKHSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.272	α = 90
b = 56.342	β = 93.89
c = 52.095	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Vetting, M.W., Bonanno, J.B., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary