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- PDB-4b1b: Crystal structure of Plasmodium falciparum oxidised Thioredoxin R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b1b | ||||||
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Title | Crystal structure of Plasmodium falciparum oxidised Thioredoxin Reductase at 2.9 angstrom | ||||||
![]() | THIOREDOXIN REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / FAD / NADPH / THIOL-MEDIATED REDOX METABOLISM / CLASS-I PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE / MALARIA | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boumis, G. / Giardina, G. / Dimastrogiovanni, D. / Angelucci, F. / Saccoccia, F. / Brunori, M. / Bellelli, A. / Miele, A.E. | ||||||
![]() | ![]() Title: Crystal Structure of Plasmodium Falciparum Thioredoxin Reductase, a Validated Drug Target. Authors: Boumis, G. / Giardina, G. / Angelucci, F. / Bellelli, A. / Brunori, M. / Dimastrogiovanni, D. / Saccoccia, F. / Miele, A.E. | ||||||
History |
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Remark 700 | SHEET SHEET RECORDS MODIFIED TO REPRESENT AUTHORS' DETAILED ANALYSIS. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.6 KB | Display | ![]() |
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PDB format | ![]() | 143.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 932 KB | Display | ![]() |
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Full document | ![]() | 977.1 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zkqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59781.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-541 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ISOLATE FCH-5 / Plasmid: PGEX-4T-1 / Production host: ![]() ![]() References: UniProt: Q25861, thioredoxin-disulfide reductase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | ADDITIONAL GLY -1 AND SER 0 ARE DERIVED FROM FUSION TAG CLEAVAGE. MET 1 IS MISSING DUE TO INSERTION ...ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.34 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 16% (W/V) PEG 4000, 0.1 M TRIS/HCL, PH 8.5, 0.2 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→15.67 Å / Num. obs: 27908 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 2.9→3.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.02 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZKQ Resolution: 2.9→46.91 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.83 / SU B: 19.092 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -1 TO 37, 175-17, 428-456, 506-541 HAVE NOT BEEN MODELLED BECAUSE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→46.91 Å
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Refine LS restraints |
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