+Open data
-Basic information
Entry | Database: PDB / ID: 1o8w | ||||||
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Title | Radiation-reduced Tryparedoxin-I | ||||||
Components | TRYPAREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / TRYPAREDOXIN-I / SYNCHROTRON RADIATION / DISULFIDE BONDS TRYPAREDOXIN / CRITHIDIA FASCICULATA / THIOREDOXIN / TRYPANOSOME / ANOMALOUS DISPERSION / OXIDATIVE STRESS | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus Similarity search - Function | ||||||
Biological species | CRITHIDIA FASCICULATA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Alphey, M.S. / Bond, C.S. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Tryparedoxins from Crithidia Fasciculata and Trypanosoma Brucei: Photoreduction of the Redox Disulfide Using Synchrotron Radiation and Evidence for a Conformational Switch Implicated in Function Authors: Alphey, M.S. / Gabrielsen, M. / Micossi, E. / Leonard, G. / Mcsweeney, S.M. / Ravelli, R.B.G. / Tetaud, E. / Fairlamb, A.H. / Bond, C.S. / Hunter, W.N. #1: Journal: J.Biol.Chem. / Year: 1999 Title: The High Resolution Structure of Recombinant Crithidia Fasciculata Tryparedoxin-I Authors: Alphey, M.S. / Leonard, G. / Gourley, D.G. / Tetaud, E. / Fairlamb, A.H. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o8w.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o8w.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1o8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o8w_validation.pdf.gz | 363.7 KB | Display | wwPDB validaton report |
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Full document | 1o8w_full_validation.pdf.gz | 363.7 KB | Display | |
Data in XML | 1o8w_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1o8w_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8w ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8w | HTTPS FTP |
-Related structure data
Related structure data | 1o73C 1o7uC 1o85C 1o8xC 1oc8C 1oc9C 1qk8S 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
#1: Protein | Mass: 16498.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O96438 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.23 % |
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Crystal grow | pH: 8.2 / Details: pH 8.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 15786 / % possible obs: 96 % / Redundancy: 2 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.4 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1QK8 Resolution: 1.7→41.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.293 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.17 Å
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Refine LS restraints |
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