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Yorodumi- PDB-4n10: Crystal structure of plasmodium falciparum oxidized glutaredoxin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n10 | ||||||
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Title | Crystal structure of plasmodium falciparum oxidized glutaredoxin 1 (PfGrx1) complexed with cisplatin | ||||||
Components | Glutaredoxin | ||||||
Keywords | OXIDOREDUCTASE / Glutathione / Active site / TRX FOLD / Redox Enzyme / Pt-SAD / cisplatin | ||||||
Function / homology | Function and homology information protein-disulfide reductase (glutathione) activity / Interconversion of nucleotide di- and triphosphates / glutathione disulfide oxidoreductase activity / antioxidant activity Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.87 Å | ||||||
Authors | Yogavel, M. / Sharma, A. | ||||||
Citation | Journal: To be Published Title: Interaction of Cisplatin with plasmodium falciparum Glutaredoxin 1 Authors: Yogavel, M. / Tripathi, T. / Rahlfs, S. / Becker, K. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n10.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n10.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n10 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n10 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12436.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: GRX1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q9NLB2, arsenate reductase (glutathione/glutaredoxin) | ||||
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#2: Chemical | ChemComp-MPO / | ||||
#3: Chemical | ChemComp-MPD / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | CPT A 204 AND CPT A 205 ARE IN ALTERNATE CONFORMATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % / Mosaicity: 0.573 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.5%(W/V) PEG1000, 12.5%(W/V) PEG3350, 12.5%(V/V) MPD, 0.02M AMINO ACIDS, 0.1M MOPS/HEPES SODIUM,, pH 7.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 2, 2013 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→50 Å / Num. all: 9916 / Num. obs: 9906 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 29.98 Å2 / Rmerge(I) obs: 0.045 / Χ2: 1.355 / Net I/σ(I): 18.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→23.349 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7874 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 26.83 / 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: 88.4 Å2 / Biso mean: 30.6244 Å2 / Biso min: 17.83 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→23.349 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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