+Open data
-Basic information
Entry | Database: PDB / ID: 8rxo | ||||||
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Title | ACDC domain of Plasmodium falciparum AP2-I transcription factor | ||||||
Components | AP2 domain transcription factor AP2-I | ||||||
Keywords | TRANSCRIPTION / AP2-coincident domain mainly at the C-terminus / Orthogonal four helix bundle | ||||||
Function / homology | AP2-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-I Function and homology information | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å | ||||||
Authors | Nessler, S. / Le Berre, M. / Li De La Sierra, I. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rxo.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rxo.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 8rxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rxo_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 8rxo_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 8rxo_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 8rxo_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/8rxo ftp://data.pdbj.org/pub/pdb/validation_reports/rx/8rxo | HTTPS FTP |
-Related structure data
Related structure data | 8rwuC 8rxaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17648.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1007700 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3-Gold / References: UniProt: Q8IJW6 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1,5 M AmSO4, 0,1 M Sodium Hepes pH 7.5, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 78 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.998→50 Å / Num. obs: 8421 / % possible obs: 99.9 % / Redundancy: 21 % / CC1/2: 0.999 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.198 / Net I/σ(I): 12.81 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.998→49.46 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.998→49.46 Å
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Refine LS restraints |
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LS refinement shell |
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