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- PDB-1zc9: The crystal structure of dialkylglycine decarboxylase complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zc9 | ||||||
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Title | The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine 5-phosphate | ||||||
![]() | 2,2-dialkylglycine decarboxylase | ||||||
![]() | LYASE / DGD complex with Pyridoxal 5-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 | ![]() ![]() | ||||||
![]() | Fogle, E.J. / Liu, W. / Toney, M.D. | ||||||
![]() | ![]() Title: Role of q52 in catalysis of decarboxylation and transamination in dialkylglycine decarboxylase. Authors: Fogle, E.J. / Liu, W. / Woon, S.T. / Keller, J.W. / Toney, M.D. | ||||||
History |
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Remark 999 | SEQUENCE As indicated by authors,the first residue methionine is missing in the database and the ... SEQUENCE As indicated by authors,the first residue methionine is missing in the database and the two other residues that conflict with the database are correct. The discrepancy is due to a mistake in the database when the protein was first sequenced. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z3zC ![]() 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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Unit cell |
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Components
#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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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PMP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MES, PEG4000, PLP, pH 6.4, 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: Jun 4, 2004 |
Radiation | Monochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 39335 / Num. obs: 38428 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DKA Resolution: 2→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Xplor file |
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