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Open data
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Basic information
Entry | Database: PDB / ID: 4cw9 | ||||||
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Title | Entamoeba histolytica thiredoxin C34S mutant | ||||||
![]() | THIOREDOXIN | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parsonage, D. / Kells, P.M. / Vieira, D.F. / Hirata, K. / Debnath, A. / Poole, L.B. / McKerrow, J.H. / Reed, S.L. / Podust, L.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 40.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Plasmid: PET17B / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | 6XHIS TAG ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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