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- PDB-7cim: Crystal structure of L-methionine decarboxylase from Streptomyces... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cim | ||||||
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Title | Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with 3-methlythiopropylamine (geminal diamine form). | ||||||
![]() | L-methionine decarboxylase | ||||||
![]() | LYASE / decarboxylase / PLP-Dependent Enzymes | ||||||
Function / homology | Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Chem-G0F / 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 | ![]() | 218 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cifSC ![]() 7cigC ![]() 7ciiC ![]() 7cijC 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: 61477.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET-52b / Production host: ![]() ![]() #2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.66 % |
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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: Jun 27, 2019 |
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: 88135 / % possible obs: 98.1 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.084 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2 / Num. unique obs: 27664 / CC1/2: 0.87 / Rpim(I) all: 0.519 / % possible all: 95.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CIF Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.007 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.918 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→19.96 Å
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Refine LS restraints |
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