4MJZ | pdb_00004mjz

2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.

• PDB DOI: https://doi.org/10.2210/pdb4MJZ/pdb

• Classification: LYASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-04 Released: 2013-09-25 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Ruan, J., Ngo, H., Shuvalova, L., Dubrovska, I., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.246 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.

Minasov, G., Wawrzak, Z., Ruan, J., Ngo, H., Shuvalova, L., Dubrovska, I., 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)

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: 70.72 kDa 
• Atom Count: 4,519 
• Modeled Residue Count: 580 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	324	Toxoplasma gondii	Mutation(s): 0  Gene Names: TGGT1_010340 EC: 4.1.1.23
UniProt
Find proteins for B6KBH9 (Toxoplasma gondii (strain ATCC 50861 / VEG)) Explore B6KBH9  Go to UniProtKB:  B6KBH9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NO3	F [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.246 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34mjz

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.477	α = 90
b = 115.477	β = 90
c = 152.055	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Minasov, G., Wawrzak, Z., Ruan, J., Ngo, H., Shuvalova, L., Dubrovska, I., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description