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Yorodumi- PDB-4ccq: Crystal structure of the thioredoxin reductase from Entamoeba his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ccq | ||||||
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Title | Crystal structure of the thioredoxin reductase from Entamoeba histolytica with NADP | ||||||
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: 1.5 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 | 4ccq.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ccq.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ccq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4ccq ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4ccq | HTTPS FTP |
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-Related structure data
Related structure data | 4a5lSC 4a65C 4cbqC 4ccrC 4cw9C 4up3C 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33779.598 Da / Num. of mol.: 2 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 |
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-Non-polymers , 5 types, 872 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: 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: 2.29 Å3/Da / Density % sol: 46.7 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 M LITHIUM ACETATE, 20% PEG 3350, pH 7 |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011 / 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: 1.5→103.52 Å / Num. obs: 96810 / % possible obs: 95.7 % / Observed criterion σ(I): 0.5 / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A5L Resolution: 1.5→103.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NICOTINAMIDE MOIETY OF NADP IN CHAIN B 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.972 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→103.52 Å
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Refine LS restraints |
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