5IM2

Crystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate

• PDB DOI: https://doi.org/10.2210/pdb5IM2/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rhodoferax ferrireducens T118
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-05 Released: 2016-03-23 
• Deposition Author(s): Vetting, M.W., 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: 1.70 Å
• R-Value Free: 0.199 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Crystal structure of a TRAP solute binding protein from Rhodoferax ferrireducens T118 (Rfer_2570, TARGET EFI-510210) in complex with copurified benzoate

Vetting, M.W., 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: 42.26 kDa 
• Atom Count: 2,754 
• Modelled Residue Count: 322 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation pathway signal	A	385	Rhodoferax ferrireducens T118	Mutation(s): 0  Gene Names: Rfer_2570
UniProt
Find proteins for Q21VB6 (Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)) Explore Q21VB6  Go to UniProtKB:  Q21VB6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	B [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.199 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.014	α = 90
b = 71.864	β = 90
c = 78.603	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Vetting, M.W., 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: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description