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Yorodumi- PDB-5l37: The structure of the pentameric shell protein MSM0273 from the RM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l37 | ||||||
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Title | The structure of the pentameric shell protein MSM0273 from the RMM microcompartment | ||||||
Components | MSM0273 | ||||||
Keywords | STRUCTURAL PROTEIN / bacterial microcompartment / pentameric shell protein | ||||||
Function / homology | EutN/Ccml / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Ethanolamine utilization protein EutN Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mallette, E. / Kimber, M.S. | ||||||
Funding support | Canada, 1items
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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 | 5l37.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l37.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 5l37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l37 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l37 | HTTPS FTP |
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-Related structure data
Related structure data | 5l38C 5l39C 5suhC 2qw7S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 10118.270 Da / Num. of mol.: 5 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_0273, MSMEI_0266 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0QP50 #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: 1.96 Å3/Da / Density % sol: 37.14 % / Description: hexagonal prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 90 mM Na acetate, 1.8 M NaCl, 10mM TCEP |
-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: 1.6→45.8 Å / Num. obs: 52789 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.735 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qw7 Resolution: 1.6→45.8 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→45.8 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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