2RCY | pdb_00002rcy

Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound

• PDB DOI: https://doi.org/10.2210/pdb2RCY/pdb

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


• Deposited: 2007-09-20 Released: 2007-10-23 
• Deposition Author(s): Wernimont, A.K., Lew, J., Lin, Y.H., Ren, H., Sun, X., Khuu, C., Hassanali, A., Wasney, G., Zhao, Y., Kozieradzki, I., Schapira, M., Bochkarev, A., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.245 (Depositor) 
• R-Value Observed: 
  0.247 (Depositor) 

Literature

Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound.

Wernimont, A.K., Lew, J., Lin, Y.H., Ren, H., Sun, X., Khuu, C., Hassanali, A., Zhao, Y., Kozieradzki, I., Schapira, M., Bochkarev, A., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Hui, R., Artz, J.D., Amani, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 148.03 kDa 
• Atom Count: 10,098 
• Modeled Residue Count: 1,268 
• Deposited Residue Count: 1,310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrroline carboxylate reductase	A, B, C, D, E	262	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: MAL13P1.284 EC: 1.5.1.2
UniProt
Find proteins for Q8IDC6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IDC6  Go to UniProtKB:  Q8IDC6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	G [auth A], J [auth B], L [auth C], N [auth D], P [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	H [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], I [auth B], M [auth D], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.289 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.245 (Depositor) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.207	α = 90
b = 113.741	β = 105.71
c = 82.651	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Wernimont, A.K., Lew, J., Lin, Y.H., Ren, H., Sun, X., Khuu, C., Hassanali, A., Wasney, G., Zhao, Y., Kozieradzki, I., Schapira, M., Bochkarev, A., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Hui, R., Artz, J.D., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary