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Yorodumi- PDB-2w0h: X ray structure of Leishmania infantum Trypanothione reductase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w0h | ||||||
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Title | X ray structure of Leishmania infantum Trypanothione reductase in complex with antimony and NADPH | ||||||
Components | TRYPANOTHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FAD / LEISHAMNIA / ANTIMONIALS / FLAVOPROTEIN / REDUCED NADPH / REDOX-ACTIVE CENTER / TRYPANOTHIONE METABOLISM | ||||||
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 Å | ||||||
Authors | Baiocco, P. / Colotti, G. / Franceschini, S. / Ilari, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Molecular Basis of Antimony Treatment in Leishmaniasis. Authors: Baiocco, P. / Colotti, G. / Franceschini, S. / Ilari, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0h.cif.gz | 198.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0h.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w0h_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2w0h_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2w0h_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 2w0h_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0h ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0h | HTTPS FTP |
-Related structure data
Related structure data | 2jk6C 1feaS C: citing same article (ref.) S: Starting model for refinement |
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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:
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 34 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 74 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 2.2 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5, 25 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 12, 2008 |
Radiation | Monochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 3→48 Å / Num. obs: 44389 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FEA Resolution: 3→103.14 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.972 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 1.252 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 21 RESIDUES OF THE SEQUENCE ARE MISSING IN THE STRUCTURE
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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: 70.03 Å2
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Refinement step | Cycle: LAST / Resolution: 3→103.14 Å
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Refine LS restraints |
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