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- PDB-1zob: Crystal structure of dialkylglycine decarboxylases bound with cal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zob | ||||||
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Title | Crystal structure of dialkylglycine decarboxylases bound with calcium ion | ||||||
![]() | 2,2-dialkylglycine decarboxylase | ||||||
![]() | LYASE / decarboxylase / pyridoxal phosphate | ||||||
Function / homology | ![]() 2,2-dialkylglycine decarboxylase (pyruvate) / 2,2-dialkylglycine decarboxylase (pyruvate) activity / L-alanine catabolic process, by transamination / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, W. / Toney, M.D. | ||||||
![]() | ![]() Title: Crystal structures of dialkylglycine decarboxylase bound with cesium ion and calcium ion Authors: Liu, W. / Toney, M.D. | ||||||
History |
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Remark 999 | SEQUENCE According to the author His15 and Glu81 are native residues in the protein and there is an ...SEQUENCE According to the author His15 and Glu81 are native residues in the protein and there is an error in the database sequence due to the mistake in the initial protein sequencing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.6 KB | Display | ![]() |
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Full document | ![]() | 473.7 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zodC ![]() 1dkaS S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the six fold axis: Y, X, 1/3-Z |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46577.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate) |
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-Non-polymers , 5 types, 68 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-PLP / |
#5: Chemical | ChemComp-MES / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG4K, MES, PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER / Detector: CCD / Date: Jul 15, 2004 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 15215 / Num. obs: 14258 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.75→2.88 Å / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DKA Resolution: 2.75→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.75→30 Å
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Refine LS restraints |
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