+Open data
-Basic information
Entry | Database: PDB / ID: 3d22 | ||||||
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Title | Crystal structure of a poplar thioredoxin h mutant, PtTrxh4C61S | ||||||
Components | Thioredoxin H-type | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin h / Electron transport / Cytoplasm / Redox-active center / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Populus trichocarpa x Populus deltoides (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Koh, C.S. / Didierjean, C. / Corbier, C. / Rouhier, N. / Jacquot, J.P. / Gelhaye, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: An Atypical Catalytic Mechanism Involving Three Cysteines of Thioredoxin. Authors: Koh, C.S. / Navrot, N. / Didierjean, C. / Rouhier, N. / Hirasawa, M. / Knaff, D.B. / Wingsle, G. / Samian, R. / Jacquot, J.P. / Corbier, C. / Gelhaye, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d22.cif.gz | 41.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d22.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d22 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d22 | HTTPS FTP |
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-Related 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: 15678.719 Da / Num. of mol.: 1 / Mutation: C61S, K62R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa x Populus deltoides (plant) Plasmid: pSBET / Production host: Escherichia coli (E. coli) / References: UniProt: P85801 |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 1.91 Å3/Da / Density % sol: 35.75 % |
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 8.2 Details: 1.0 M sodium / potassium phosphate , pH 8.2, microbatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.24 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2005 / Details: mirrors |
Radiation | Monochromator: Fixed exit double crystal Si [111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 16333 / Num. obs: 16333 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wild-type PtTrxh4 Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.426 / SU ML: 0.052 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.087 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.691 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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