+Open data
-Basic information
Entry | Database: PDB / ID: 4cw9 | ||||||
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Title | Entamoeba histolytica thiredoxin C34S mutant | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis Similarity search - Function | ||||||
Biological species | ENTAMOEBA HISTOLYTICA HM-3\:IMSS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Parsonage, D. / Kells, P.M. / Vieira, D.F. / 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 | 4cw9.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cw9.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/4cw9 ftp://data.pdbj.org/pub/pdb/validation_reports/cw/4cw9 | HTTPS FTP |
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-Related structure data
Related structure data | 4a5lC 4a65C 4cbqC 4ccqC 4ccrC 4up3C 2vimS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12457.250 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DISULFIDE BOND BETWEEN CYS31 A AND CYS31 B Source: (gene. exp.) ENTAMOEBA HISTOLYTICA HM-3\:IMSS (eukaryote) Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LYR0, UniProt: M7X179*PLUS #2: Water | ChemComp-HOH / | Sequence details | 6XHIS TAG ENGINEERED | |
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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: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.2 M NACL, 25% PEG 3350 O.1 M BIS-TRIS, PH 5.5 |
-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: Mar 26, 2014 / 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: 1.84→47.95 Å / Num. obs: 14832 / % possible obs: 82.3 % / Observed criterion σ(I): 0.5 / Redundancy: 3.5 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 40.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VIM Resolution: 1.84→44.43 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.88 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.19 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→44.43 Å
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Refine LS restraints |
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