3DKU

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1.

Hong, M.K.Kim, J.K.Jung, J.H.Jung, J.W.Choi, J.Y.Kang, L.W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative phosphohydrolaseABCDEFGH153Escherichia coli APEC O1Mutation(s): 0 
Gene Names: nudJEcok1_10240APECO1_216
EC: 3.6.1
Find proteins for A1AA28 (Escherichia coli O1:K1 / APEC)
Explore A1AA28 
Go to UniProtKB:  A1AA28
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.96α = 90
b = 70.521β = 103.3
c = 145.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Derived calculations