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- PDB-3wqe: D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wqe | ||||||
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Title | D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with D-allothreonine | ||||||
![]() | D-threo-3-hydroxyaspartate dehydratase | ||||||
![]() | LYASE / dehydratase / PLP | ||||||
Function / homology | ![]() threo-3-hydroxy-D-aspartate ammonia-lyase / ammonia-lyase activity / D-serine ammonia-lyase activity / D-serine catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasutake, Y. / Matsumoto, Y. / Wada, M. | ||||||
![]() | ![]() Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D- ...Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate Authors: Matsumoto, Y. / Yasutake, Y. / Takeda, Y. / Tamura, T. / Yokota, A. / Wada, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315 KB | Display | ![]() |
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PDB format | ![]() | 255.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.3 KB | Display | ![]() |
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Full document | ![]() | 493.6 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wqcC ![]() 3wqdC ![]() 3wqfC ![]() 3wqgC ![]() 4pb3C ![]() 4pb4C ![]() 4pb5C C: citing same article ( |
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Similar 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: 41549.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: B2DFG5, threo-3-hydroxy-D-aspartate ammonia-lyase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | SG ATOM OF CYS 353 AND NE2 ATOM OF HIS 351 ARE COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 13% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 130617 / Num. obs: 130617 / % possible obs: 99.9 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 33.65 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 6.89 / Num. unique all: 6506 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.073 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.33 Å
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Refine LS restraints |
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