4GNJ | pdb_00004gnj

Crystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase

• PDB DOI: https://doi.org/10.2210/pdb4GNJ/pdb

• Classification: ISOMERASE
• Organism(s): Leishmania sp. 'siamensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-17 Released: 2013-09-11 
• Deposition Author(s): Kuaprasert, B., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Mungthin, M., Leelayoova, S., Leartsakulpanich, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.199 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase

Kuaprasert, B., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Mungthin, M., Leelayoova, S., Leartsakulpanich, U.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.66 kDa 
• Atom Count: 4,202 
• Modeled Residue Count: 493 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	271	Leishmania sp. 'siamensis	Mutation(s): 0  Gene Names: Lstim, tim EC: 5.3.1.1
UniProt
Find proteins for I2APN2 (Leishmania sp. 'siamensis') Explore I2APN2  Go to UniProtKB:  I2APN2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARS	C [auth A], D [auth B]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.199 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.58	α = 90
b = 78.79	β = 101.15
c = 83.16	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Kuaprasert, B., Riangrungroj, P., Pornthanakasem, W., Suginta, W., Mungthin, M., Leelayoova, S., Leartsakulpanich, U.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description