6TCV

Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc2Asn substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-beta-N-acetylglucosaminidase F1A [auth B]451Bacteroides thetaiotaomicron VPI-5482Mutation(s): 2 
Gene Names: BT_3987
UniProt
Find proteins for Q8A0N4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A0N4 
Go to UniProtKB:  Q8A0N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A0N4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]11N-Glycosylation
Glycosylation Resources
GlyTouCan:  G60230HH
GlyCosmos:  G60230HH
GlyGen:  G60230HH
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.495α = 90
b = 115.495β = 90
c = 97.422γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
XDSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary