6SY0

Structure of the Plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with two SPE2 half-sites

• PDB DOI:  https://doi.org/10.2210/pdb6SY0/pdb
• NAKB: 6SY0

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


• Deposited: 2019-09-26 Released: 2020-10-07 
• Deposition Author(s): Reiter, D., Kantsadi, A., Vakonakis, I.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 

Literature

Structural and functional analysis of the Plasmodium falciparum SIP2 DNA binding domain

Niederwieser, I., Reiter, D., Kantsadi, A., Voss, T., Vakonakis, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82.96 kDa 
• Atom Count: 5,331 
• Modelled Residue Count: 481 
• Deposited Residue Count: 525 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor with AP2 domain(S)	A, B, C	139	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_0604100
UniProt
Find proteins for C6KSN9 (Plasmodium falciparum (isolate 3D7)) Explore C6KSN9  Go to UniProtKB:  C6KSN9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')	D [auth E], E [auth F], F [auth G], G [auth H], H [auth K], I [auth L]	18	Plasmodium falciparum 3D7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B, C	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.318 
• R-Value Work: 0.274 
• R-Value Observed: 0.276 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.35	α = 90
b = 43.72	β = 92.17
c = 153.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Reiter, D., Kantsadi, A., Vakonakis, I.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release