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- PDB-6sy0: Structure of the Plasmodium falciparum SIP2 DNA-binding AP2 tande... -

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Basic information

Entry
Database: PDB / ID: 6sy0
TitleStructure of the Plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with two SPE2 half-sites
Components
  • DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
  • Transcription factor with AP2 domain(S)
KeywordsDNA BINDING PROTEIN / Plasmodium falciparum malaria Subtelomeric repeat var genes
Function / homologytelomeric DNA binding / nuclear periphery / DNA / DNA (> 10) / AP2 domain transcription factor
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.102 Å
AuthorsReiter, D. / Kantsadi, A. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Structural and functional analysis of the Plasmodium falciparum SIP2 DNA binding domain
Authors: Niederwieser, I. / Reiter, D. / Kantsadi, A. / Voss, T. / Vakonakis, I.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor with AP2 domain(S)
B: Transcription factor with AP2 domain(S)
C: Transcription factor with AP2 domain(S)
E: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
K: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
L: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)82,9609
Polymers82,9609
Non-polymers00
Water00
1
B: Transcription factor with AP2 domain(S)
E: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription factor with AP2 domain(S)
F: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-21 kcal/mol
Surface area14350 Å2
MethodPISA
3
C: Transcription factor with AP2 domain(S)
K: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
L: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-14 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.350, 43.720, 153.710
Angle α, β, γ (deg.)90.00, 92.17, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Transcription factor with AP2 domain(S)


Mass: 16618.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0604100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6KSN9
#2: DNA chain
DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Mass: 5517.566 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote)
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.16 M calcium acetate 100 mM cacodylic acid 6.5% w/v PEG 8000 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 3.1→153.6 Å / Num. obs: 19852 / % possible obs: 97 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Net I/σ(I): 15.24
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 1912 / CC1/2: 0.927 / Rrim(I) all: 1.164 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.102→43.931 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3184 963 5 %0
Rwork0.2736 ---
obs0.2758 18302 96.72 %-
Refinement stepCycle: LAST / Resolution: 3.102→43.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 2196 0 0 5331

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