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Yorodumi- PDB-4adw: CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM TRYPANOTHIONE REDUCTASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4adw | ||||||
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Title | CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM TRYPANOTHIONE REDUCTASE IN COMPLEX WITH NADPH AND TRYPANOTHIONE | ||||||
Components | TRYPANOTHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / INHIBITION MECHANISM | ||||||
Function / homology | Function and homology information trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | LEISHMANIA INFANTUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å | ||||||
Authors | Baiocco, P. / Ilari, A. / Colotti, G. / Malatesta, F. / Fiorillo, A. | ||||||
Citation | Journal: Chemmedchem / Year: 2013 Title: Inhibition of Leishmania Infantum Trypanothione Reductase by Azole-Based Compounds: A Comparative Analysis with its Physiological Substrate by X-Ray Crystallography. Authors: Baiocco, P. / Poce, G. / Alfonso, S. / Cocozza, M. / Porretta, G.C. / Colotti, G. / Biava, M. / Moraca, F. / Botta, M. / Yardley, V. / Fiorillo, A. / Lantella, A. / Malatesta, F. / Ilari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4adw.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4adw.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 4adw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4adw_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4adw_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4adw_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 4adw_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adw ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adw | HTTPS FTP |
-Related structure data
Related structure data | 4apnC 2jk6S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
#1: Protein | Mass: 55257.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA INFANTUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: A4HSF7, trypanothione-disulfide reductase #2: Chemical | #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 74 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1 M TRIS PH 8.5, 2.2 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 23097 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JK6 Resolution: 3.61→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.866 / SU B: 41.015 / SU ML: 0.57 / Cross valid method: THROUGHOUT / ESU R Free: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.272 Å2
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Refinement step | Cycle: LAST / Resolution: 3.61→50 Å
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Refine LS restraints |
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