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Open data
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Basic information
Entry | Database: PDB / ID: 4mzc | |||||||||
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Title | Atomic Resolution Structure of PfGrx1 | |||||||||
![]() | Glutaredoxin | |||||||||
![]() | OXIDOREDUCTASE / glutathione / sulfur-SAD / active site / plasticity / TRX fold / redox enzyme | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yogavel, M. / Sharma, A. | |||||||||
![]() | ![]() Title: Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins. Authors: Yogavel, M. / Tripathi, T. / Gupta, A. / Banday, M.M. / Rahlfs, S. / Becker, K. / Belrhali, H. / Sharma, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hjmSC ![]() 4mzbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Strain: 3D7 / Gene: GRX1, PFC0271c / Plasmid: PQE30 / Production host: ![]() ![]() References: UniProt: Q9NLB2, arsenate reductase (glutathione/glutaredoxin) |
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#2: Chemical | ChemComp-MPO / |
#3: Chemical | ChemComp-MPD / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.16 % |
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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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2012 / Details: mirrors |
Radiation | Monochromator: Si(III) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72932 Å / Relative weight: 1 |
Reflection | Resolution: 0.949→50 Å / Num. all: 70202 / Num. obs: 69290 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21 % / Biso Wilson estimate: 7.85 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 43.02 |
Reflection shell | Resolution: 0.949→0.97 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 6.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4HJM Resolution: 0.949→23.985 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.9617 / SU ML: 0.05 / σ(F): 1.34 / Phase error: 7.21 / 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: 104.55 Å2 / Biso mean: 13.3007 Å2 / Biso min: 4.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.949→23.985 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: 25
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