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Yorodumi- PDB-5suh: The structure of double ringed trimeric shell protein MSM0271 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5suh | ||||||
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Title | The structure of double ringed trimeric shell protein MSM0271 from the RMM microcompartment | ||||||
Components | MSM0271 protein | ||||||
Keywords | STRUCTURAL PROTEIN / Bacterial microcompartment / shell / BMC-FP | ||||||
Function / homology | BMC (bacterial microcompartment) domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Mallette, E. / Kimber, M.S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport. Authors: Mallette, E. / Kimber, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5suh.cif.gz | 245.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5suh.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 5suh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/5suh ftp://data.pdbj.org/pub/pdb/validation_reports/su/5suh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26019.549 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0271, MSMEI_0264 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QP48 #2: 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: 2.72 Å3/Da / Density % sol: 54.71 % / Description: hexagonal prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10 mg/mL protein, 0.8 M Na/K tartrate, 0.1 M Tris, 0.5% (w/v) PEG 2000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.2 Å / Num. obs: 24387 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 69.4 Å2 / CC1/2: 0.997 / Rsym value: 0.133 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.752 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MSM0275 Resolution: 2.7→47.139 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.139 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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