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- PDB-4pb5: D-threo-3-hydroxyaspartate dehydratase H351A mutant complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pb5 | ||||||
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Title | D-threo-3-hydroxyaspartate dehydratase H351A mutant complexed with L-erythro-3-hydroxyaspartate | ||||||
![]() | D-threo-3-hydroxyaspartate dehydratase | ||||||
![]() | LYASE / PLP enzyme / dehydratase / metalloprotein | ||||||
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. | ||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 308.6 KB | Display | ![]() |
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PDB format | ![]() | 250.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.1 KB | Display | ![]() |
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Full document | ![]() | 495.7 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wqcC ![]() 3wqdC ![]() 3wqeC ![]() 3wqfC ![]() 3wqgC ![]() 4pb3C ![]() 4pb4C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41482.047 Da / Num. of mol.: 2 / Mutation: H351A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: B2DFG5, threo-3-hydroxy-D-aspartate ammonia-lyase |
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-Non-polymers , 5 types, 476 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BH2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BH2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350, Tris-HCl. MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 77555 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.12 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 7 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→40.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.085 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.002 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→40.46 Å
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Refine LS restraints |
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