4KZK | pdb_00004kzk

The structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis

• PDB DOI: https://doi.org/10.2210/pdb4KZK/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2013-06-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

The structure of the periplasmic L-arabinose binding protein from Burkholderia thailandensis

Clifton, M.C., Fairman, J.W.

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: 35.75 kDa 
• Atom Count: 2,619 
• Modeled Residue Count: 301 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-arabinose ABC transporter, periplasmic L-arabinose-binding protein	A	337	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: BTH_II1196
UniProt
Find proteins for Q2T607 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T607  Go to UniProtKB:  Q2T607

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34KZK

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.77	α = 90
b = 51.82	β = 107.34
c = 59.22	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary