+Open data
-Basic information
Entry | Database: PDB / ID: 5v76 | ||||||
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Title | Structure of Haliangium ochraceum BMC-T HO-3341 | ||||||
Components | Microcompartments protein | ||||||
Keywords | STRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENTS | ||||||
Function / homology | BMC (bacterial microcompartment) domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Microcompartments protein Function and homology information | ||||||
Biological species | Haliangium ochraceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Sutter, M. / Paasch, B. / Zarzycki, J. / Aussignargues, C. / Kerfeld, C.A. | ||||||
Citation | Journal: Science / Year: 2017 Title: Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. Authors: Markus Sutter / Basil Greber / Clement Aussignargues / Cheryl A Kerfeld / Abstract: Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable ...Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v76.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v76.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 5v76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v76 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v76 | HTTPS FTP |
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-Related structure data
Related structure data | 8747C 5v74C 5v75C 4ht5S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21871.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria) Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_3341 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LV02 #2: Chemical | ChemComp-GOL / | #3: 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: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M cacodylate pH 6.5 1.25M citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→39.09 Å / Num. obs: 65376 / % possible obs: 99.92 % / Redundancy: 42.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 44 % / Rmerge(I) obs: 1.797 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9459 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HT5 Resolution: 1.55→39.09 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→39.09 Å
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Refine LS restraints |
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LS refinement shell |
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