6SW4 | pdb_00006sw4

The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus

• PDB DOI: https://doi.org/10.2210/pdb6SW4/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-19 Released: 2020-10-14 
• Deposition Author(s): Lansky, S., Salama, R., Lavid, N., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus

Lansky, S., Salama, R., Lavid, N., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 74.08 kDa 
• Atom Count: 4,725 
• Modeled Residue Count: 587 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arabinose binding protein	A, B	335	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: araP
UniProt
Find proteins for B3EYL5 (Geobacillus stearothermophilus) Explore B3EYL5  Go to UniProtKB:  B3EYL5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.79	α = 90
b = 95.6	β = 90
c = 128.94	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Lansky, S., Salama, R., Lavid, N., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description