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- PDB-4i7a: GrpN pentameric microcompartment shell protein from Rhodospirillu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i7a | ||||||
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Title | GrpN pentameric microcompartment shell protein from Rhodospirillum rubrum | ||||||
![]() | Ethanolamine utilization protein EutN/carboxysome structural protein Ccml | ||||||
![]() | STRUCTURAL PROTEIN / microcompartments / ccmL / eutN / glycyl radical propanediol microcompartment | ||||||
Function / homology | EutN/Ccml / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wheatley, N.M. / Gidaniyan, S.D. / Cascio, D. / Yeates, T.O. | ||||||
![]() | ![]() Title: Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins. Authors: Wheatley, N.M. / Gidaniyan, S.D. / Liu, Y. / Cascio, D. / Yeates, T.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.2 KB | Display | ![]() |
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PDB format | ![]() | 127.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qw7S 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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Unit cell |
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Components
#1: Protein | Mass: 9880.153 Da / Num. of mol.: 5 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: 2.89 Å3/Da / Density % sol: 57.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.2, 1.5 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→106.57 Å / Num. obs: 9248 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 73.556 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.02 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QW7 Resolution: 3.2→19.789 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7272 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.25 Å2 / Biso mean: 87.6177 Å2 / Biso min: 51.97 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.789 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 47.2819 Å / Origin y: 29.815 Å / Origin z: 0.0653 Å
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Refinement TLS group |
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