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- PDB-8rxa: ACDC domain of AP2-O5 from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 8rxa
TitleACDC domain of AP2-O5 from Plasmodium falciparum
ComponentsAP2 domain transcription factor AP2-O5, putative
KeywordsTRANSCRIPTION / AP2-coincident domain mainly at the C-terminus / Orthogonal four helix bundle
Function / homologyAP2-coincident, C-terminal domain / AP2-coincident C-terminal / AP2/ERF domain / AP2 domain / DNA-binding transcription factor activity / DNA binding / nucleus / AP2 domain transcription factor AP2-O5, putative
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsNessler, S. / Le Berre, M. / Gallay Li de la Sierra, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2024
Title: Structural characterization of the ACDC domain from ApiAP2 proteins of the malaria parasite.
Authors: Le Berre, M. / Tubiana, T. / Reutersward Waldner, P. / Lazar, N. / Li de la Sierra, I. / Santos, J.M. / Llinas, M. / Nessler, S.
History
DepositionFeb 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP2 domain transcription factor AP2-O5, putative
B: AP2 domain transcription factor AP2-O5, putative


Theoretical massNumber of molelcules
Total (without water)23,5292
Polymers23,5292
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Eluted as a monomer on a SEC column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-22 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.930, 108.930, 34.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-676-

ASN

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Components

#1: Protein AP2 domain transcription factor AP2-O5, putative


Mass: 11764.653 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1449500 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3-Gold / References: UniProt: Q8IKY0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG400, 0.1 M MES pH 6.5, 0.1 M Sodium acetate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 22718 / % possible obs: 99.5 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.059 / Net I/σ(I): 22.24
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.75-1.860.93735100.9410.9741
1.86-1.990.52234080.9860.5421
1.99-2.140.26532030.9940.2771
2.14-2.350.14329170.9970.1481
2.35-2.620.08826990.9980.0921
2.62-3.030.0623530.9990.0631
3.03-3.70.04520430.9990.0471
3.7-5.210.03816120.9990.0391

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→39.998 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2099 4.97 %
Rwork0.2099 --
obs0.2118 22661 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→39.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 0 47 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141585
X-RAY DIFFRACTIONf_angle_d1.3042127
X-RAY DIFFRACTIONf_dihedral_angle_d19.4051002
X-RAY DIFFRACTIONf_chiral_restr0.065241
X-RAY DIFFRACTIONf_plane_restr0.008266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7511-1.79180.36751310.32622514X-RAY DIFFRACTION91
1.7918-1.83660.36041450.28292683X-RAY DIFFRACTION99
1.8366-1.88630.29691430.25412684X-RAY DIFFRACTION100
1.8863-1.94180.30471400.23062636X-RAY DIFFRACTION99
1.9418-2.00450.31681430.22752743X-RAY DIFFRACTION100
2.0045-2.07610.27631390.21172639X-RAY DIFFRACTION99
2.0761-2.15920.26161380.19592669X-RAY DIFFRACTION100
2.1592-2.25750.24261420.1922743X-RAY DIFFRACTION100
2.2575-2.37650.26391410.19422658X-RAY DIFFRACTION100
2.3765-2.52540.23041340.20722693X-RAY DIFFRACTION100
2.5254-2.72030.29271440.21192723X-RAY DIFFRACTION100
2.7203-2.9940.28951340.23152675X-RAY DIFFRACTION100
2.994-3.4270.28381430.23062705X-RAY DIFFRACTION100
3.427-4.31690.21591430.19572694X-RAY DIFFRACTION100
4.3169-39.9980.20471390.1952697X-RAY DIFFRACTION100

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