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- PDB-5hwm: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hwm | ||||||
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Title | Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid | ||||||
![]() | Probable 5-dehydro-4-deoxyglucarate dehydratase | ||||||
![]() | LYASE / decarboxylating / dehydratase / TIM-barrel | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Taberman, H. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 443.7 KB | Display | ![]() |
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PDB format | ![]() | 383.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486 KB | Display | ![]() |
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Full document | ![]() | 502.1 KB | Display | |
Data in XML | ![]() | 48.8 KB | Display | |
Data in CIF | ![]() | 69.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() Gene: Atu3140, AGR_L_3338 / Production host: ![]() ![]() References: UniProt: Q8UB77, 5-dehydro-4-deoxyglucarate dehydratase #2: Chemical | ChemComp-OOG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.39 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 12, 2013 |
Radiation | Monochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.9 Å / Num. obs: 76785 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 92.8 |
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Processing
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Refinement | Resolution: 2.097→47.883 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.99 / 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: 2.097→47.883 Å
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Refine LS restraints |
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LS refinement shell |
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