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Open data
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Basic information
Entry | Database: PDB / ID: 3mpy | ||||||
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Title | Structure of EUTM in 2-D protein membrane | ||||||
![]() | Ethanolamine utilization protein eutM | ||||||
![]() | MEMBRANE PROTEIN / Bacterial microcompartment / shell protein / ethanolamine ammonia lyase / carboxysome | ||||||
Function / homology | ![]() ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / protein hexamerization / structural molecule activity / 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 | ![]() | 30.5 KB | Display | ![]() |
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PDB format | ![]() | 20.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mpvC ![]() 3mpwC ![]() 2a1bS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 10706.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2 M ammoniumsulfate, 100 mM sodium acetate, pH 4.6, 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: Jun 11, 2009 / Details: Rh coated flat mirror. | |||||||||||||||
Radiation | Monochromator: SI 111 (side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→17.3 Å / Num. obs: 4477 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rsym value: 0.078 / Net I/σ(I): 20.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2A1B (RESIDUES 2-90) Resolution: 2→17.29 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.144 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA SET WAS TWINNED AND REFINEMENT WAS CARRIED OUT ACCORDINGLY WITH THE PROGRAM REFMAC. OCCUPANCIES OF THE SULFATES ARE LESS THAN ONE DUE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA SET WAS TWINNED AND REFINEMENT WAS CARRIED OUT ACCORDINGLY WITH THE PROGRAM REFMAC. OCCUPANCIES OF THE SULFATES ARE LESS THAN ONE DUE TO THEIR SPECIAL POSITIONS. THE N-TERMINAL METHIONINE AND THE HIS-TAGS WERE 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: 40.223 Å2
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Refinement step | Cycle: LAST / Resolution: 2→17.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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