+Open data
-Basic information
Entry | Database: PDB / ID: 1gy9 | ||||||
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Title | Taurine/alpha-ketoglutarate Dioxygenase from Escherichia coli | ||||||
Components | ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / TAURINE / SULPHUR METABOLISM / OXYGENASE / ALPHA-KETOGLUTARATE / TAUD / TFDA | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Elkins, J.M. / Burzlaff, N.I. / Ryle, M.J. / Lloyd, J.S. / Clifton, I.J. / Baldwin, J.E. / Hausinger, R.P. / Roach, P.L. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: X-Ray Crystal Structure of Escherichia Coli Taurine/Alpha-Ketoglutarate Dioxygenase Complexed to Ferrous Iron and Substrates. Authors: Elkins, J.M. / Ryle, M.J. / Clifton, I.J. / Dunning Hotopp, J.C. / Lloyd, J.S. / Burzlaff, N.I. / Baldwin, J.E. / Hausinger, R.P. / Roach, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gy9.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gy9.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gy9 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gy9 | HTTPS FTP |
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-Related structure data
Related structure data | 1gqwSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.85598, 0.51686, -0.01248), Vector: |
-Components
#1: Protein | Mass: 32453.467 Da / Num. of mol.: 2 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: Chemical | #5: Water | ChemComp-HOH / | Compound details | CONVERTS ALPHA KETOGLUTAR | |
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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: 3 Å3/Da / Density % sol: 60 % |
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Crystal grow | pH: 7.5 Details: 20-28% PEG1000, 20% ETHYLENE GLYCOL, 75MM IMIDAZOLE PH7.5, PROTEIN SOLUTION LOADED WITH FE(II), ALPHA-KETOGLUTARATE, TAURINE, DITHIOTHREITOL, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.935 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90 Å / Num. obs: 28679 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GQW Resolution: 2.5→45.18 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.51 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES WITH DISORDERED SIDE-CHAINS WERE MODELED AS ALANINE
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.18 Å
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Refine LS restraints |
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