Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.44 kDa 
• Atom Count: 1402 
• Modelled Residue Count: 157 
• Deposited Residue Count: 172 
• Unique protein chains: 1

2AR1

Structure of Hypothetical protein from Leishmania major

• PDB DOI: 10.2210/pdb2AR1/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-18 Released: 2005-08-30 
• Deposition Author(s): Arakaki, T.L., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

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

• PubMed: 16511295 
• DOI: 10.1107/S1744309106005902
• Primary Citation of Related Structures:  
  2AR1


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A	172	Leishmania major	Mutation(s): 0  Gene Names: LmjF36.6870, LMJF_36_6870
UniProt
Find proteins for Q4Q067 (Leishmania major) Explore Q4Q067  Go to UniProtKB:  Q4Q067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 31.199	α = 90
b = 64.607	β = 90
c = 72.559	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-18 
• Released Date: 2005-08-30 
Deposition Author(s): Arakaki, T.L., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• 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