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Yorodumi- PDB-5hwn: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hwn | |||||||||
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Title | Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate | |||||||||
Components | Probable 5-dehydro-4-deoxyglucarate dehydratase | |||||||||
Keywords | LYASE / decarboxylating / dehydratase / TIM-barrel | |||||||||
Function / homology | Function and homology information 5-dehydro-4-deoxyglucarate dehydratase / 5-dehydro-4-deoxyglucarate dehydratase activity / D-glucarate catabolic process / 4-hydroxy-tetrahydrodipicolinate synthase activity Similarity search - Function | |||||||||
Biological species | Agrobacterium fabrum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.499 Å | |||||||||
Authors | Taberman, H. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J. | |||||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase. Authors: Taberman, H. / Andberg, M. / Parkkinen, T. / Janis, J. / Penttila, M. / Hakulinen, N. / Koivula, A. / Rouvinen, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hwn.cif.gz | 500.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwn.ent.gz | 418.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwn ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwn | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33562.363 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Gene: Atu3140, AGR_L_3338 / Production host: Escherichia coli (E. coli) References: UniProt: Q8UB77, 5-dehydro-4-deoxyglucarate dehydratase #2: Chemical | ChemComp-PYR / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FMT / #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: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: BICINE, sodium formate, PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.09 Å / Num. obs: 214991 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4 |
-Processing
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Refinement | Resolution: 1.499→48.087 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→48.087 Å
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Refine LS restraints |
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LS refinement shell |
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