3VXC | pdb_00003vxc

Crystal Structure of Xylobiose-BxlE complex from Streptomyces thermoviolaceus OPC-520

• PDB DOI: https://doi.org/10.2210/pdb3VXC/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: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.98 kDa 
• Atom Count: 6,578 
• Modeled Residue Count: 796 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	C, D	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.672	α = 90
b = 163.157	β = 90
c = 42.931	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Structure summary