+Open data
-Basic information
Entry | Database: PDB / ID: 7div | ||||||
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Title | Structure of PfGrx1 in the intermediate state with cadmium | ||||||
Components | Glutaredoxin | ||||||
Keywords | OXIDOREDUCTASE / REDOX ENZYME / TRX FOLD / GLUTATHIONE / Cd-SAD | ||||||
Function / homology | Function and homology information protein-disulfide reductase (glutathione) activity / Interconversion of nucleotide di- and triphosphates / glutathione disulfide oxidoreductase activity / antioxidant activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.64 Å | ||||||
Authors | Manickam, Y. / Sharma, A. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Interaction of metals with PfGrx1 Authors: Manickam, Y. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7div.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7div.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 7div.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7div_validation.pdf.gz | 898.3 KB | Display | wwPDB validaton report |
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Full document | 7div_full_validation.pdf.gz | 898.3 KB | Display | |
Data in XML | 7div_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7div_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/7div ftp://data.pdbj.org/pub/pdb/validation_reports/di/7div | HTTPS FTP |
-Related structure data
Related structure data | 7dikC 7dilC 7dimC 7dinC 7dioC 7dipC 7diqC 7dirC 7disC 7ditC 7diuC 7diwC 7dizC 7dj0C C: citing same article (ref.) |
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Similar 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 (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_0306300 / Plasmid: PQE30 / Production host: Escherichia coli M15 (bacteria) References: UniProt: Q9NLB2, protein-disulfide reductase (glutathione) | ||||
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#2: Chemical | ChemComp-MPO / | ||||
#3: Chemical | ChemComp-MPD / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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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, 0.02 M amino acids, 0.1 M MOPS/HEPES sodium |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 17, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→50 Å / Num. obs: 14205 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.259 / Net I/σ(I): 15.3 / Num. measured all: 123926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.64→24.099 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.54 / 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: 85.73 Å2 / Biso mean: 23.8185 Å2 / Biso min: 12.38 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.64→24.099 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -23.1038 Å / Origin y: 10.1112 Å / Origin z: -5.4253 Å
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Refinement TLS group |
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