3VXC | pdb_00003vxc

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

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) 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative sugar-binding lipoprotein
A, B
436Streptomyces thermoviolaceusMutation(s): 0 
Gene Names: bxlD
UniProt
Find proteins for Q76BU9 (Streptomyces thermoviolaceus)
Explore Q76BU9 
Go to UniProtKB:  Q76BU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76BU9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Biologically Interesting Molecules (External Reference) 1 Unique
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 = 103.672α = 90
b = 163.157β = 90
c = 42.931γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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