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Yorodumi- PDB-8rwu: ACDC domain of the AP2-I transcription factor from Plasmodium vivax -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rwu | ||||||
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Title | ACDC domain of the AP2-I transcription factor from Plasmodium vivax | ||||||
Components | AP2 domain transcription factor AP2-I, putative | ||||||
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, putative Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.152 Å | ||||||
Authors | Nessler, S. / Le Berre, M. / Gallay 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 | 8rwu.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rwu.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 8rwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rwu_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 8rwu_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 8rwu_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 8rwu_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/8rwu ftp://data.pdbj.org/pub/pdb/validation_reports/rw/8rwu | HTTPS FTP |
-Related structure data
Related structure data | 8rxaC 8rxoC 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: 22151.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVP01_0807400 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3-Gold / References: UniProt: A0A564ZT73 |
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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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 400 , 0.1 M Mes pH 6.5, 0.1 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 78 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980118 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 10, 2023 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980118 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.15→50 Å / Num. obs: 7133 / % possible obs: 99.7 % / Redundancy: 25 % / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.118 / Net I/σ(I): 21.53 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.152→48.623 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.22 / 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 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 124.79 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.152→48.623 Å
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Refine LS restraints |
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LS refinement shell |
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