+Open data
-Basic information
Entry | Database: PDB / ID: 7u2v | ||||||
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Title | Plasmodium falciparum Cyt c2 DSD | ||||||
Components | Cytochrome c2 | ||||||
Keywords | ELECTRON TRANSPORT / alpha helix / heme / DSD / domain-swapped dimer | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / mitochondrial respirasome / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Model details | Plasmodium falciparum Cyt c2 forming a domain-swapped dimer complex | ||||||
Authors | Hill, C.P. / Wienkers, H.J. / Whitby, F.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites Authors: Espino-Sanchez, T.J. / Wienkers, H. / Marvin, R.G. / Nalder, S.A. / Garcia-Guerrero, A.E. / VanNatta, P.E. / Jami-Alahmadi, Y. / Mixon Blackwell, A. / Whitby, F.G. / Wohlschlegel, J.A. / ...Authors: Espino-Sanchez, T.J. / Wienkers, H. / Marvin, R.G. / Nalder, S.A. / Garcia-Guerrero, A.E. / VanNatta, P.E. / Jami-Alahmadi, Y. / Mixon Blackwell, A. / Whitby, F.G. / Wohlschlegel, J.A. / Kieber-Emmons, M.T. / Hill, C.P. / Sigala, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u2v.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u2v.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 7u2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u2v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7u2v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7u2v_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 7u2v_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/7u2v ftp://data.pdbj.org/pub/pdb/validation_reports/u2/7u2v | HTTPS FTP |
-Related structure data
Related structure data | 7txeC 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: 17990.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1311700 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I6T6 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1.73816 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.73816 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→39.92 Å / Num. obs: 8552 / % possible obs: 84.2 % / Redundancy: 47.6 % / Biso Wilson estimate: 5.8 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.064 / Rrim(I) all: 0.416 / Net I/σ(I): 20.2 / Num. measured all: 407151 / Scaling rejects: 2777 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→39.92 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.17 / 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 max: 130.86 Å2 / Biso mean: 25.3151 Å2 / Biso min: 0.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→39.92 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 0.0926 Å / Origin y: 21.8733 Å / Origin z: 18.6359 Å
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Refinement TLS group |
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