Structure of Hypothetical protein from Leishmania major

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major.

Arakaki, T.Le Trong, I.Phizicky, E.Quartley, E.DeTitta, G.Luft, J.Lauricella, A.Anderson, L.Kalyuzhniy, O.Worthey, E.Myler, P.J.Kim, D.Baker, D.Hol, W.G.Merritt, E.A.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 175-179

  • DOI: https://doi.org/10.1107/S1744309106005902
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The gene product of structural genomics target Lmaj006129 from Leishmania major codes for a 164-residue protein of unknown function. When SeMet expression of the full-length gene product failed, several truncation variants were created with the aid of Ginzu, a domain-prediction method. 11 truncations were selected for expression, purification and crystallization based upon secondary-structure elements and disorder. The structure of one of these variants, Lmaj006129AAH, was solved by multiple-wavelength anomalous diffraction (MAD) using ELVES, an automatic protein crystal structure-determination system. This model was then successfully used as a molecular-replacement probe for the parent full-length target, Lmaj006129AAA. The final structure of Lmaj006129AAA was refined to an R value of 0.185 (Rfree = 0.229) at 1.60 A resolution. Structure and sequence comparisons based on Lmaj006129AAA suggest that proteins belonging to Pfam sequence families PF04543 and PF01878 may share a common ligand-binding motif.

  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein172Leishmania majorMutation(s): 0 
Gene Names: LmjF36.6870
Find proteins for Q4Q067 (Leishmania major)
Explore Q4Q067 
Go to UniProtKB:  Q4Q067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Q067
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.199α = 90
b = 64.607β = 90
c = 72.559γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description