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- PDB-3gfh: Crystal structure of EUTL shell protein of the bacterial ethanola... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gfh | ||||||
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Title | Crystal structure of EUTL shell protein of the bacterial ethanolamine micrompartment | ||||||
![]() | Ethanolamine utilization protein eutL | ||||||
![]() | STRUCTURAL PROTEIN / bacterial mircocompartment / shell protein / ethanolamine | ||||||
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. / Nikolakakis, K. / Ohtaki, A. | ||||||
![]() | ![]() 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 | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.5 KB | Display | ![]() |
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Full document | ![]() | 481.2 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 2M Nacl, 100mM phosphate, MES buffer pH6.5, 5% PEG 400, 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 / Details: SI-MIRRORS | |||||||||||||||
Radiation | 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: 1.95→19.95 Å / Num. obs: 51500 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 | |||||||||||||||
Reflection shell | Resolution: 1.95→2.3 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.46 / % possible all: 74.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MODEL WAS DERIVED FROM FITTING INTO A 3.5 A SAD DENSITY DERIVED FROM TWO MERCURY ATOMS. Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.866 / SU B: 9.162 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE STRUCTURE WAS REFINED AGAINST TWINNED DATA AS PUBLISHED. The data is hemohedral twinning with twinning operators: (h,-h-k,-l) and corresponding twinned fractions: 0.575, 0.425. RESIDUES ...Details: THE STRUCTURE WAS REFINED AGAINST TWINNED DATA AS PUBLISHED. The data is hemohedral twinning with twinning operators: (h,-h-k,-l) and corresponding twinned fractions: 0.575, 0.425. RESIDUES 2-216 COULD BE FITTED RELIABLY INTO THE ELECTRON DENSITY MAP. 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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