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Yorodumi- PDB-1ep8: CRYSTAL STRUCTURE OF A MUTATED THIOREDOXIN, D30A, FROM CHLAMYDOMO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ep8 | ||||||
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Title | CRYSTAL STRUCTURE OF A MUTATED THIOREDOXIN, D30A, FROM CHLAMYDOMONAS REINHARDTII | ||||||
Components | THIOREDOXIN CH1, H-TYPE | ||||||
Keywords | ELECTRON TRANSPORT / mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Menchise, V. / Corbier, C. / Didierjean, C. / Saviano, M. / Benedetti, E. / Jacquot, J.P. / Aubry, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2001 Title: Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism. Authors: Menchise, V. / Corbier, C. / Didierjean, C. / Saviano, M. / Benedetti, E. / Jacquot, J.P. / Aubry, A. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: NMR Solution Structure of an Oxidized Thioredoxin h from the Eukaryotic Green alga Chlamydomonas reinhardtii Authors: Mittard, V. / Blackledge, M.J. / Stein, M. / Jacquot, J. / Marion, D. / Lancelin, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ep8.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ep8.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ep8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ep8_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 1ep8_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 1ep8_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1ep8_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1ep8 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1ep8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11683.524 Da / Num. of mol.: 2 / Mutation: D30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P80028 #2: 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: 2.22 Å3/Da / Density % sol: 44.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, PEG 10000, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 53351 / Num. obs: 10823 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Num. unique all: 1006 / % possible all: 91.6 |
Reflection | *PLUS Num. measured all: 53351 |
Reflection shell | *PLUS % possible obs: 91.6 % / Mean I/σ(I) obs: 6.2 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 Details: The two molecules, A and B, have been refined independently, without imposing non-crystallographic 2-fold axis.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.196 / Rfactor Rfree: 0.22 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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