1TC5 | pdb_00001tc5

Structural Analysis of a probable eukaryotic D-amino acid tRNA deacylase

• PDB DOI: https://doi.org/10.2210/pdb1TC5/pdb

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


• Deposited: 2004-05-20 Released: 2004-06-08 
• Deposition Author(s): Robien, M.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of LMAJ005534AAA, a probable eukaryotic D-amino acid tRNA deacylase from Leishmania major

Robien, M.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.1 kDa 
• Atom Count: 6,204 
• Modeled Residue Count: 746 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable eukaryotic D-amino acid tRNA deacylase, LMAJ005534AAA	A, B, C, D	194	Leishmania major	Mutation(s): 0  Gene Names: L4171.5 EC: 3.1
UniProt
Find proteins for P84066 (Leishmania major) Explore P84066  Go to UniProtKB:  P84066

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.479	α = 90
b = 67.465	β = 90
c = 174.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Robien, M.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2004-06-08
  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: 2018-01-31
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-04-03
  Changes: Refinement description