5IBQ

Crystal structure of an ABC solute binding protein from Rhizobium etli CFN 42 (RHE_PF00037,TARGET EFI-511357) in complex with alpha-D-apiose

• PDB DOI: https://doi.org/10.2210/pdb5IBQ/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Rhizobium etli CFN 42
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-22 Released: 2016-04-20 
• Deposition Author(s): Vetting, M.W., Carter, M.S., 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: 1.20 Å
• R-Value Free: 0.164 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Crystal structure of an ABC solute binding protein from Rhizobium etli CFN 42 (RHE_PF00037,TARGET EFI-511357) in complex with alpha-D-apiose

Vetting, M.W., Carter, M.S., 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: 33.29 kDa 
• Atom Count: 2,630 
• Modelled Residue Count: 287 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribose ABC transporter, substrate-binding protein	A	310	Rhizobium etli CFN 42	Mutation(s): 0  Gene Names: RHE_PF00037
UniProt
Find proteins for Q2JZQ5 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2JZQ5  Go to UniProtKB:  Q2JZQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XXM	B [auth A]	3-C-(hydroxylmethyl)-alpha-D-erythrofuranose C5 H10 O5 ASNHGEVAWNWCRQ-VAYJURFESA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.164 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.272	α = 90
b = 36.924	β = 118.02
c = 95.619	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Vetting, M.W., Carter, M.S., 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: 2016-04-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary