+Open data
-Basic information
Entry | Database: PDB / ID: 4mzb | |||||||||
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Title | Crystal structure of Grx1 from Plasmodium falciparum | |||||||||
Components | Glutaredoxin | |||||||||
Keywords | OXIDOREDUCTASE / glutathione / sulfur-SAD / active site / plasticity / TRX fold / redox enzyme | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.038 Å | |||||||||
Authors | Yogavel, M. / Sharma, A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mzb.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mzb.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mzb_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 4mzb_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 4mzb_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 4mzb_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/4mzb ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mzb | HTTPS FTP |
-Related structure data
Related structure data | 4hjmSC 4mzcC S: Starting model for refinement 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 (malaria parasite P. falciparum) Strain: 3D7 / Gene: GRX1, PFC0271c / 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.82656 Å |
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: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 1.038→50 Å / Num. all: 53655 / Num. obs: 53655 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.6 % / Biso Wilson estimate: 8.27 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 52.6 |
Reflection shell | Resolution: 1.038→1.08 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HJM Resolution: 1.038→23.023 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.9522 / SU ML: 0.06 / σ(F): 1.34 / Phase error: 8.96 / 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: 95.93 Å2 / Biso mean: 14.351 Å2 / Biso min: 4.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.038→23.023 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: 19
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