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Yorodumi- PDB-7aoj: Plasmoredoxin, a redox-active protein unique for malaria parasites -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aoj | ||||||
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Title | Plasmoredoxin, a redox-active protein unique for malaria parasites | ||||||
Components | Plasmoredoxin | ||||||
Keywords | OXIDOREDUCTASE / Malaria / Plasmodium falciparum / thioredoxin superfamily / redox metabolism | ||||||
Function / homology | Thioredoxin-like / Thioredoxin-like fold / protein disulfide isomerase activity / Thioredoxin-like superfamily / Plasmoredoxin Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å | ||||||
Authors | Fritz-Wolf, K. / Bathke, J. / Rahlfs, S. / Becker, K. | ||||||
Funding support | 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: Crystal structure of plasmoredoxin, a redox-active protein unique for malaria parasites. Authors: Fritz-Wolf, K. / Bathke, J. / Rahlfs, S. / Becker, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aoj.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aoj.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 7aoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aoj_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 7aoj_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 7aoj_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7aoj_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aoj ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aoj | HTTPS FTP |
-Related structure data
Related structure data | 7aooC 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: 21720.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_0303600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I224 | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1,6 ammonium sulfate, 0.5 M glycine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→19.45 Å / Num. obs: 25144 / % possible obs: 99.16 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.0155 / Rrim(I) all: 0.0593 / Rsym value: 0.057 / Net I/σ(I): 33.87 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.3433 / Mean I/σ(I) obs: 4 / Num. unique obs: 2336 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.1802 / Rrim(I) all: 0.3908 / Rsym value: 0.339 / % possible all: 92.23 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.63→19.45 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5279 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 28.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→19.45 Å
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Refine LS restraints |
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LS refinement shell |
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