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- PDB-1d7u: Crystal structure of the complex of 2,2-dialkylglycine decarboxyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d7u | ||||||
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Title | Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS | ||||||
![]() | PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)) | ||||||
![]() | LYASE / ENZYME COMPLEXES / CATALYTIC MECHANISM / DECARBOXYLATION INHIBITOR | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Malashkevich, V.N. / Toney, M.D. / Strop, P. / Keller, J. / Jansonius, J.N. | ||||||
![]() | ![]() Title: Crystal structures of dialkylglycine decarboxylase inhibitor complexes. Authors: Malashkevich, V.N. / Strop, P. / Keller, J.W. / Jansonius, J.N. / Toney, M.D. #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 | ![]() | 99 KB | Display | ![]() |
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PDB format | ![]() | 73.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 460.8 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d7rC ![]() 1d7sC ![]() 1d7vC ![]() 2dkbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46495.320 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-NA / |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-LCS / [ |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 26, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35 Å / Num. obs: 42043 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.398 / % possible all: 73.3 |
Reflection | *PLUS Redundancy: 3.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DKB Resolution: 1.95→10 Å / Isotropic thermal model: RESTRAINED / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 164.5 Å2 / ksol: 0.67 e/Å3 | ||||||||||||
Displacement parameters | Biso mean: 35.26 Å2 | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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