3VXB | pdb_00003vxb

Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520

• PDB DOI: https://doi.org/10.2210/pdb3VXB/pdb

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


• Deposited: 2012-09-11 Released: 2013-09-18 
• Deposition Author(s): Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal Structure of Xylooligosaccharide-Binding Protein from Streptomyces thermoviolaceus OPC-520: Dramatic Conformational Change with Ligand binding

Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

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: 47.08 kDa 
• Atom Count: 3,148 
• Modeled Residue Count: 399 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar-binding lipoprotein	A	436	Streptomyces thermoviolaceus	Mutation(s): 0  Gene Names: bxlD
UniProt
Find proteins for Q76BU9 (Streptomyces thermoviolaceus) Explore Q76BU9  Go to UniProtKB:  Q76BU9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.634	α = 90
b = 63.272	β = 103.05
c = 66.402	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Tomoo, K., Ishida, T., Miyamoto, K., Tsujibo, H.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations