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- PDB-7cif: Crystal structure of L-methionine decarboxylase from Streptomyces... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cif | ||||||
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Title | Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 (internal aldimine form). | ||||||
![]() | L-methionine decarboxylase | ||||||
![]() | LYASE / decarboxylase / PLP-Dependent Enzymes | ||||||
Function / homology | Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / L-methionine decarboxylase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okawa, A. / Shiba, T. / Hayashi, M. / Onoue, Y. / Murota, M. / Sato, D. / Inagaki, J. / Tamura, T. / Harada, S. / Inagaki, K. | ||||||
![]() | ![]() Title: Structural basis for substrate specificity of l-methionine decarboxylase. Authors: Okawa, A. / Shiba, T. / Hayashi, M. / Onoue, Y. / Murota, M. / Sato, D. / Inagaki, J. / Tamura, T. / Harada, S. / Inagaki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.8 KB | Display | ![]() |
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PDB format | ![]() | 175.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 462.1 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 56.8 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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Unit cell |
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Components
#1: Protein | Mass: 61705.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET-52b / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MMT buffer pH 6.0, 23.5 % (w/v) PEG1500 / PH range: 5.6-6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 86707 / % possible obs: 92.7 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.077 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 25929 / CC1/2: 0.665 / Rpim(I) all: 0.704 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.421 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→19.89 Å
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Refine LS restraints |
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