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Yorodumi- PDB-4ccr: Crystal structure of the thioredoxin reductase apoenzyme from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ccr | ||||||
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Title | Crystal structure of the thioredoxin reductase apoenzyme from Entamoeba histolytica in the absence of the NADP cofactor | ||||||
Components | THIOREDOXIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / AMOEBIASIS / REDOX METABOLISM / OXIDATIVE STRESS / AURANOFIN | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ENTAMOEBA HISTOLYTICA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Parsonage, D. / Kells, P.M. / Hirata, K. / Debnath, A. / Poole, L.B. / McKerrow, J.H. / Reed, S.L. / Podust, L.M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: X-Ray Structures of Thioredoxin and Thioredoxin Reductase from Entamoeba Histolytica and Prevailing Hypothesis of the Mechanism of Auranofin Action. Authors: Parsonage, D. / Sheng, F. / Hirata, K. / Debnath, A. / Mckerrow, J.H. / Reed, S.L. / Abagyan, R. / Poole, L.B. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ccr.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ccr.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ccr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ccr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4ccr_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4ccr_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 4ccr_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4ccr ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4ccr | HTTPS FTP |
-Related structure data
Related structure data | 4a5lC 4a65C 4cbqC 4ccqC 4cw9C 4up3C 3itjS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33779.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Plasmid: PTRCHISA / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 References: UniProt: C4LW95, thioredoxin-disulfide reductase #2: Chemical | ChemComp-AU / #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | Nonpolymer details | GOLD ION (AU): GOLD IS RELEASED BY AURANOFIN PRESENT IN CRYSTALLIZ | |
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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: 2.43 Å3/Da / Density % sol: 49.46 % Description: ISOLATED FAD- AND NADPH-BINDING DOMAINS OF SACCHAROMYCES CEREVISIAE THIOREDOXIN REDUCTASE WERE USED AS SEARCH MODELS |
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Crystal grow | pH: 7 Details: 20% PEG 3350,0.2 M AMMONIUM TARTRATE, PH 7.0; 3 MM AURANOFIN |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 29, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→91.03 Å / Num. obs: 59359 / % possible obs: 99.7 % / Observed criterion σ(I): 0.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ITJ Resolution: 2.28→91.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.016 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE NADPH-BINDING DOMAIN IN CHAIN D IS OMITTED FROM THE STRUCTURE DUE TO INSUFFICIENT ELECTRON DENSITY.
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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: 43.674 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→91.03 Å
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Refine LS restraints |
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