+Open data
-Basic information
Entry | Database: PDB / ID: 6nlu | ||||||
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Title | Circularly permuted Haliangium ochraceum BMC-H | ||||||
Components | circularly permuted BMC-H | ||||||
Keywords | STRUCTURAL PROTEIN / bacterial microcompartment | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haliangium ochraceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.607 Å | ||||||
Authors | Sutter, M. / Ferlez, B. / Kerfeld, C.A. | ||||||
Citation | Journal: Metab. Eng. / Year: 2019 Title: A designed bacterial microcompartment shell with tunable composition and precision cargo loading. Authors: Ferlez, B. / Sutter, M. / Kerfeld, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nlu.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nlu.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 6nlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nlu ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nlu | HTTPS FTP |
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-Related structure data
Related structure data | 5djbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10559.107 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haliangium ochraceum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5 #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: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.5 M Ammonium tartrate, 0.1 M sodium acetate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.607→43.58 Å / Num. obs: 51230 / % possible obs: 99.9 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.021 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.607→1.69 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 7266 / CC1/2: 0.973 / Rpim(I) all: 0.109 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DJB Resolution: 1.607→43.579 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.607→43.579 Å
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Refine LS restraints |
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LS refinement shell |
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