6SY0 | pdb_00006sy0

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.318 (Depositor), 0.311 (DCC)
R-Value Work:
0.274 (Depositor), 0.274 (DCC)
R-Value Observed:
0.276 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6SY0

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C6KSN9
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(GPGPTPGPCPAPCPCPTPAPGPGPTPGPCPAPCPC)-3')	D [auth E] E [auth F] F [auth G] G [auth H] H [auth K] D [auth E], E [auth F], F [auth G], G [auth H], H [auth K], I [auth L]	18	Plasmodium falciparum 3D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF Query on 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 (Depositor), 0.311 (DCC)
R-Value Work: 0.274 (Depositor), 0.274 (DCC)
R-Value Observed: 0.276 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-10-07
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.