4ZLV | pdb_00004zlv

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286

• PDB DOI: https://doi.org/10.2210/pdb4ZLV/pdb

• Classification: TRANSFERASE
• Organism(s): Toxoplasma gondii ME49
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-01 Released: 2015-05-20 
• Deposition Author(s): Filippova, E.V., Minasov, G., Flores, K., Van Le, H., Silverman, R.B., McLeod, R., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with the Schiff base between PLP and Lys286

Filippova, E.V., Minasov, G., Flores, K., Van Le, H., Silverman, R.B., McLeod, R., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 97.97 kDa 
• Atom Count: 7,125 
• Modeled Residue Count: 843 
• Deposited Residue Count: 882 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine aminotransferase, mitochondrial, putative	A, B	441	Toxoplasma gondii ME49	Mutation(s): 0  Gene Names: TGME49_269110 EC: 2.6.1.13
UniProt
Find proteins for S8EY38 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore S8EY38  Go to UniProtKB:  S8EY38

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34zlv

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.481	α = 100.45
b = 61.459	β = 92.39
c = 63.435	γ = 108.32

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	phasing
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Filippova, E.V., Minasov, G., Flores, K., Van Le, H., Silverman, R.B., McLeod, R., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description