5GQG

Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, galacto-N-biose complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lacto-N-biosidase
A, B
606Bifidobacterium longum subsp. longumMutation(s): 0 
Gene Names: lnbX
EC: 3.2.1.140
UniProt
Find proteins for A0A024QYS6 (Bifidobacterium longum subsp. longum)
Explore A0A024QYS6 
Go to UniProtKB:  A0A024QYS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024QYS6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan:  G01534TU
GlyCosmos:  G01534TU
GlyGen:  G01534TU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.103α = 90
b = 144.061β = 90
c = 144.445γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food IndustryJapan25010A
JSPSJapan16J09251

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Structure summary