3UOW | pdb_00003uow

Crystal Structure of PF10_0123, a GMP Synthetase from Plasmodium Falciparum

• PDB DOI: https://doi.org/10.2210/pdb3UOW/pdb

• Classification: LIGASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-17 Released: 2011-12-07 
• Deposition Author(s): Wernimont, A.K., Dong, A., Hills, T., Amani, M., Perieteanu, A., Lin, Y.H., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of PF10_0123, a GMP Synthetase from Plasmodium Falciparum

Wernimont, A.K., Dong, A., Hills, T., Amani, M., Perieteanu, A., Lin, Y.H., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R.

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: 128.91 kDa 
• Atom Count: 7,474 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthetase	A, B	556	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF10_0123 EC: 6.3.5.2
UniProt
Find proteins for Q8IJR9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJR9  Go to UniProtKB:  Q8IJR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMP	C [auth A], E [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C10 H14 N4 O9 P DCTLYFZHFGENCW-UUOKFMHZSA-O
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.158	α = 103.07
b = 67.76	β = 99.36
c = 99.825	γ = 94.33

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
macChess	data collection
DENZO	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Wernimont, A.K., Dong, A., Hills, T., Amani, M., Perieteanu, A., Lin, Y.H., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description