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Open data
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Basic information
Entry | Database: PDB / ID: 3mpv | ||||||
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Title | Structure of EUTL in the zinc-induced open form | ||||||
![]() | Ethanolamine utilization protein eutL | ||||||
![]() | MEMBRANE PROTEIN / shell protein / bacterial microcompartment / ethanolamine / carboxysome | ||||||
Function / homology | ![]() ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / structural molecule activity / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sagermann, M. / Takenoya, M. / Nikolakakis, K. | ||||||
![]() | ![]() Title: Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli. Authors: Takenoya, M. / Nikolakakis, K. / Sagermann, M. #1: ![]() Title: Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Authors: Sagermann, M. / Ohtaki, A. / Nikolakakis, 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 | ![]() | 86.9 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mpwC ![]() 3mpyC ![]() 3gfhS 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: 23633.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BME / | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 M NaCl, 100 mM phosphate, 100 mM MES buffer, 5 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009 / Details: Si III mirror | |||||||||||||||
Radiation | Monochromator: SI 111 bend crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979464 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→58.43 Å / Num. obs: 11274 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 1.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GFH Resolution: 2.6→58.38 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.85 / SU B: 14.419 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data sets for this crystal appeared twinned. refinement was carried out as described in primary citation. The N-terminal methionine as well ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data sets for this crystal appeared twinned. refinement was carried out as described in primary citation. The N-terminal methionine as well as the residues from 215B (or 216A) on (including the HIS6-tag) were not visible in the density. Likewise, the aas between residues 69 and 83 and 180-183 were also not visible in the density.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.034 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→58.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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