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- PDB-1dge: AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dge | ||||||
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Title | AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE | ||||||
![]() | DIALKYLGLYCINE DECARBOXYLASE | ||||||
![]() | LYASE | ||||||
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 | ![]() | ||||||
![]() | Hohenester, E. / Jansonius, J.N. | ||||||
![]() | ![]() Title: An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase. Authors: Hohenester, E. / Keller, J.W. / Jansonius, J.N. #1: ![]() Title: Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Sites Authors: Toney, M.D. / Hohenester, E. / Jacob, S.W. / Jansonius, J.N. #2: ![]() Title: Pseudomonas Cepacia 2,2-Dialkylglycine Decarboxylase. Sequence and Expression in Escherichia Coli of Structural and Repressor Genes Authors: Keller, J.W. / Baurick, K.B. / Rutt, G.C. / O'Malley, M.V. / Sonafrank, N.L. / Reynolds, R. / Ebbesson, L.O. / Vajdos, F.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 400.9 KB | Display | ![]() |
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Full document | ![]() | 419.4 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 18.5 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Atom site foot note | 1: ATOMS WITH WEAK DENSITY HAVE BEEN REFINED WITH ZERO WEIGHT. 2: LYS 272 IS COVALENTLY BOUND TO THE COFACTOR PLP. | ||||||||
Details | THE MOLECULE IS A TETRAMER OF IDENTICAL SUBUNITS. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH COMPRISES ONE MONOMER. THE TETRAMER CAN BE GENERATED BY CRYSTALLOGRAPHIC DYADS. APPLYING THE FOLLOWING TRANSFORMATION TO THE COORDINATES IN THIS ENTRY WILL YIELD A DIMER: MTRIX1 1 -0.500000 0.866000 0.000000 0.00000 MTRIX2 1 0.866000 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 28.87000 APPLYING THE FOLLOWING TRANSFORMATION TO THE DIMER WILL YIELD THE TETRAMER: MTRIX1 2 -1.000000 0.000000 0.000000 76.40000 MTRIX2 2 0.000000 -1.000000 0.000000 132.20000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 |
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Components
#1: Protein | Mass: 46374.145 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 | #3: Chemical | ChemComp-PLP / | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 222.873-875 1991 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 14856 / % possible obs: 97.7 % / Num. measured all: 62340 / Rmerge(I) obs: 0.108 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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