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- PDB-2dkb: DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dkb | ||||||
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Title | DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES | ||||||
![]() | 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE) | ||||||
![]() | LYASE(DECARBOXYLASE) | ||||||
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 | ![]() | ||||||
![]() | Toney, M.D. / Hohenester, E. / Jansonius, J.N. | ||||||
![]() | ![]() Title: Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites. Authors: Toney, M.D. / Hohenester, E. / Cowan, S.W. / Jansonius, J.N. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Dialkylglycine Decarboxylase, a Decarboxylating Transaminase Authors: Toney, M.D. / Keller, J.W. / Pauptit, R.A. / Jaeger, J. / Wise, M.K. / Sauder, U. / 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.A. / 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 | ![]() | 96.5 KB | Display | ![]() |
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PDB format | ![]() | 78.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: THE FOLLOWING RESIDUES HAVE WEAK ELECTRON DENSITY: 142 - 143, 346 - 347, AND 369 - 377. 2: AT SITE PLP, RESIDUE LYS 272 HAS THE COFACTOR PYRIDOXAL-5'-PHOSPHATE COVALENTLY ATTACHED TO IT. | ||||||||
Details | DGD IS A TETRAMER OF IDENTICAL SUBUNITS. THE FOLLOWING TRANSFORMATIONS WILL GENERATE THE OTHER THREE SUBUNITS OF THE TETRAMER: MTRIX1 1 -0.500000 0.866010 0.000000 0.00000 MTRIX2 1 0.866041 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 -1.000000 28.86753 MTRIX1 2 0.500000 -0.866010 0.000000 76.34753 MTRIX2 2 -0.866041 -0.500000 0.000000 132.24016 MTRIX3 2 0.000000 0.000000 -1.000000 28.86753 MTRIX1 3 -1.000000 0.000000 0.000000 76.34753 MTRIX2 3 0.000000 -1.000000 0.000000 132.24016 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 |
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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 | #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: 3.13 Å3/Da / Density % sol: 60.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging dropDetails: taken from Toney, M.D., (1991) J.Mol.Biol., 222, 873. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 32665 / % possible obs: 93 % / Rmerge(I) obs: 0.078 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→8 Å / Rfactor obs: 0.178 Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY OR REFINE TO B-FACTORS (GREATER THAN) 100 ANGSTROMS**2 HAVE A WEIGHT OF ZERO. | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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