+Open data
-Basic information
Entry | Database: PDB / ID: 1otj | ||||||
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Title | Crystal structure of APO (iron-free) TauD | ||||||
Components | Alpha-Ketoglutarate-Dependent Taurine Dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Jelly roll motif / alpha ketoglutarate-dependent dioxygenase / taurine | ||||||
Function / homology | Function and homology information taurine catabolic process / taurine dioxygenase complex / taurine dioxygenase / taurine dioxygenase activity / sulfur compound metabolic process / L-ascorbic acid binding / ferrous iron binding / protein homotetramerization / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Direct methods, MAD / Resolution: 1.9 Å | ||||||
Authors | O'Brien, J.R. / Schuller, D.J. / Yang, V.S. / Dillard, B.D. / Lanzilotta, W.N. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure Authors: O'Brien, J.R. / Schuller, D.J. / Yang, V.S. / Dillard, B.D. / Lanzilotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1otj.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1otj.ent.gz | 200.9 KB | Display | PDB format |
PDBx/mmJSON format | 1otj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1otj_validation.pdf.gz | 479.9 KB | Display | wwPDB validaton report |
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Full document | 1otj_full_validation.pdf.gz | 511.7 KB | Display | |
Data in XML | 1otj_validation.xml.gz | 52 KB | Display | |
Data in CIF | 1otj_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/1otj ftp://data.pdbj.org/pub/pdb/validation_reports/ot/1otj | 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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Details | Two biological dimers are found in the crystallographic tetramer. They are monomers A & E, and B & D. |
-Components
#1: Protein | Mass: 32453.467 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P37610, taurine dioxygenase #2: Chemical | #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 48.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: batch / pH: 8 Details: PEG 4000, Isopropanol, Sodium citrate, pH 8.0, Batch, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 21, 2002 / Details: Osmic Blue confocal mirrors |
Radiation | Monochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 105897 / Num. obs: 99459 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.049 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / Num. unique all: 600 / Rsym value: 0.34 / % possible all: 93.5 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 78.9 % / Rmerge(I) obs: 0.334 |
-Processing
Software |
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Refinement | Method to determine structure: Direct methods, MAD / Resolution: 1.9→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Num. reflection Rfree: 5034 / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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