4KDZ

Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)

Kim, J., Toro, R., Bhosle, R., Almo, S.C.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (cytidine(34)-2'-O)-methyltransferase157Escherichia coli UTI89Mutation(s): 0 
Gene Names: b3606, JW3581, trmL, UTI89_C4147, yibK
EC: 2.1.1.207
UniProt
Find proteins for Q1R4Y9 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R4Y9 
Go to UniProtKB:  Q1R4Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1R4Y9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.435α = 90
b = 84.435β = 90
c = 78.654γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description