5ULB | pdb_00005ulb

Crystal structure of sugar ABC transporter from Yersinia enterocolitica subsp. enterocolitica 8081

• PDB DOI: https://doi.org/10.2210/pdb5ULB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-24 Released: 2018-09-12 
• Deposition Author(s): Nocek, B., Bigelow, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.153 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.110 (Depositor), 0.115 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Literature

Crystal structure of sugar ABC transporter from Yersinia enterocolitica subsp. enterocolitica 8081

Nocek, B., Bigelow, L., Joachimiak, A.

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: 36.83 kDa 
• Atom Count: 3,036 
• Modeled Residue Count: 333 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar ABC transporter	A	337	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0
UniProt
Find proteins for A1JTX8 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JTX8  Go to UniProtKB:  A1JTX8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8GA	B [auth A]	5-Se-methyl-5-seleno-alpha-D-ribofuranose C6 H12 O4 Se UFNQFLPLDXICBS-KAZBKCHUSA-N
8GG	C [auth A]	5-Se-methyl-5-seleno-beta-D-ribofuranose C6 H12 O4 Se UFNQFLPLDXICBS-KVTDHHQDSA-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: 1.28 Å
• R-Value Free:  0.153 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.110 (Depositor), 0.115 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.993	α = 90
b = 55.856	β = 90
c = 119.573	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Nocek, B., Bigelow, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary