3GEK

Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

X-Ray structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113

Kuzin, A.P., Su, M., Seetharaman, R., Lee, D., Foote, E.L., Ciccosanti, C., Janjua, H., Xiao, R., Nair, R., Rost, B., Acton, T.B., Everett, J.K., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative thioesterase yhdA
A, B, C, D
146Lactococcus lactis subsp. lactis Il1403Mutation(s): 7 
Gene Names: L131, L131392, LL0726, yhdA
UniProt
Find proteins for Q9CHK5 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CHK5 
Go to UniProtKB:  Q9CHK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CHK5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.948α = 90
b = 64.056β = 90
c = 144.657γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing

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: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection