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Yorodumi- PDB-2dw6: Crystal structure of the mutant K184A of D-Tartrate Dehydratase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dw6 | ||||||
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Title | Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate | ||||||
Components | Bll6730 protein | ||||||
Keywords | LYASE / D-Tartrate Dehydratase / Enolase superfamily / D-tartrate / L-tartrate | ||||||
Function / homology | Function and homology information D(-)-tartrate dehydratase / D(-)-tartrate dehydratase activity / protein homooligomerization / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Yew, W.S. / Wood, B.M. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Evolution of Enzymatic Activities in the Enolase Superfamily: d-Tartrate Dehydratase from Bradyrhizobium japonicum Authors: Yew, W.S. / Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dw6.cif.gz | 311.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dw6.ent.gz | 253.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/2dw6 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/2dw6 | HTTPS FTP |
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-Related structure data
Related structure data | 2dw7C 1tzzS 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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Details | The biological assembly is a dimer. There are two dimers in the asymmetric unit. |
-Components
#1: Protein | Mass: 43053.008 Da / Num. of mol.: 4 / Mutation: K184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q89FH0, D(-)-tartrate dehydratase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-TLA / | #5: 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: 4.24 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.8M K/Na L-tartrate, 0.1M Tris.HCl, 0.5% PEG MME 5000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2006 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 115401 / Num. obs: 115401 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TZZ Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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