+Open data
-Basic information
Entry | Database: PDB / ID: 3mpv | ||||||
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Title | Structure of EUTL in the zinc-induced open form | ||||||
Components | Ethanolamine utilization protein eutL | ||||||
Keywords | MEMBRANE PROTEIN / shell protein / bacterial microcompartment / ethanolamine / carboxysome | ||||||
Function / homology | Function and homology information ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / structural molecule activity / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sagermann, M. / Takenoya, M. / Nikolakakis, K. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2010 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: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mpv.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mpv.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mpv ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mpv | HTTPS FTP |
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-Related structure data
Related structure data | 3mpwC 3mpyC 3gfhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2439, eutL, JW2432, yffJ / Plasmid: TOPO101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P76541 #2: Chemical | ChemComp-BME / | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979464 Å | |||||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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