3JWP | pdb_00003jwp

Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb3JWP/pdb

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


• Deposited: 2009-09-18 Released: 2009-10-20 
• Deposition Author(s): Wernimont, A.K., Hutchinson, A., Lin, Y.H., MacKenzie, F., Senisterra, G., Allali-Hassanali, A., Vedadi, M., Ravichandran, M., Cossar, D., Kozieradzki, I., Zhao, Y., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Qiu, W., Brand, V., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.274 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of Plasmodium falciparum SIR2A (PF13_0152) in complex with AMP

Wernimont, A.K., Hutchinson, A., Lin, Y.H., MacKenzie, F., Senisterra, G., Allali-Hassanali, A., Vedadi, M., Ravichandran, M., Cossar, D., Kozieradzki, I., Zhao, Y., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Qiu, W., Brand, V.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.19 kDa 
• Atom Count: 1,925 
• Modeled Residue Count: 255 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein sir2 homologue	A	265	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF13_0152, Sir2 EC: 2.3.1
UniProt
Find proteins for Q8IE47 (Plasmodium falciparum (isolate 3D7)) Explore Q8IE47  Go to UniProtKB:  Q8IE47

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.274 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.564	α = 90
b = 106.564	β = 90
c = 44.968	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Adxv	data processing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Wernimont, A.K., Hutchinson, A., Lin, Y.H., MacKenzie, F., Senisterra, G., Allali-Hassanali, A., Vedadi, M., Ravichandran, M., Cossar, D., Kozieradzki, I., Zhao, Y., Schapira, M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Qiu, W., Brand, V., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary