+Open data
-Basic information
Entry | Database: PDB / ID: 4ags | ||||||
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Title | Leishmania TDR1 - a unique trimeric glutathione transferase | ||||||
Components | THIOL-DEPENDENT REDUCTASE 1 | ||||||
Keywords | TRANSFERASE / LEISHMANIASIS / DE-GLUATHIONYLATION | ||||||
Function / homology | Function and homology information cell redox homeostasis / electron transfer activity / identical protein binding Similarity search - Function | ||||||
Biological species | LEISHMANIA INFANTUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Fyfe, P.K. / Westrop, G.D. / Silva, A.M. / Coombs, G.H. / Hunter, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Leishmania Tdr1 Structure, a Unique Trimeric Glutathione Transferase Capable of Deglutathionylation and Antimonial Prodrug Activation. Authors: Fyfe, P.K. / Westrop, G.D. / Silva, A.M. / Coombs, G.H. / Hunter, W.N. #1: Journal: Biochem.J. / Year: 2004 Title: Reduction of Anti-Leishmanial Pentavalent Antimonial Drugs by a Parasite-Specific Thiol-Dependent Reductase, Tdr1. Authors: Denton, H. / Mcgregor, J.C. / Coombs, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ags.cif.gz | 582.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ags.ent.gz | 502 KB | Display | PDB format |
PDBx/mmJSON format | 4ags.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4ags ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4ags | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 53195.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA INFANTUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834 (DE3) / References: UniProt: A4I8P2 #2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.8 Å / Num. obs: 74464 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.9 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.633 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.404 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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