8UTA

yjdF riboswitch from R. gauvreauii in complex with proflavine bound to Fab BL3-6 S97N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for promiscuity in ligand recognition by yjdF riboswitch.

Krochmal, D.Roman, C.Lewicka, A.Shao, Y.Piccirilli, J.A.

(2024) Cell Discov 10: 37-37


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6 S97N heavy chainC [auth A],
D [auth H]
233Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6 S97N light chainE [auth B],
F [auth L]
215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
yjdF RNA (R. gauvreauii)A [auth N],
B [auth R]
128Ruminococcus gauvreauii
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.873α = 87.25
b = 75.138β = 87.99
c = 95.727γ = 87.72
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM149336

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references