5OCP | pdb_00005ocp

The periplasmic binding protein component of the arabinose ABC transporter from Shewanella sp. ANA-3 bound to alpha and beta-L-arabinofuranose

• PDB DOI: https://doi.org/10.2210/pdb5OCP/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Shewanella sp. ANA-3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-03 Released: 2018-08-01 
• Deposition Author(s): Herman, R.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

CHARACTERISATION OF A FURANOSE SPECIFIC ABC TRANSPORTER ESSENTIAL FOR ARABINOSE UTILISATION FROM THE LIGNOCELLULOSE DEGRADING BACTERIUM SHEWANELLA SP. ANA-3

Herman, R., Drousiotis, K., Wilkinson, A.J., Thomas, G.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.01 kDa 
• Atom Count: 5,171 
• Modeled Residue Count: 604 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A, B	302	Shewanella sp. ANA-3	Mutation(s): 0  Gene Names: Shewana3_2073

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUB (Subject of Investigation/LOI)	J [auth A], O [auth B]	beta-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-KLVWXMOXSA-N
AHR (Subject of Investigation/LOI)	I [auth A], N [auth B]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.917	α = 90
b = 86.327	β = 90
c = 87.282	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Herman, R.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N01040X/1

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 2.0: 2018-12-19
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.2: 2024-11-20
  Changes: Structure summary