+Open data
-Basic information
Entry | Database: PDB / ID: 6ob5 | |||||||||
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Title | Computationally-designed, modular sense/response system (S3-2D) | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / computational protein design / chemically-induced dimerization / biosensor / Rosetta | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) unidentified (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.208 Å | |||||||||
Authors | Thompson, M.C. / Glasgow, A.A. / Huang, Y.M. / Fraser, J.S. / Kortemme, T. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: Computational design of a modular protein sense-response system. Authors: Glasgow, A.A. / Huang, Y.M. / Mandell, D.J. / Thompson, M. / Ritterson, R. / Loshbaugh, A.L. / Pellegrino, J. / Krivacic, C. / Pache, R.A. / Barlow, K.A. / Ollikainen, N. / Jeon, D. / Kelly, ...Authors: Glasgow, A.A. / Huang, Y.M. / Mandell, D.J. / Thompson, M. / Ritterson, R. / Loshbaugh, A.L. / Pellegrino, J. / Krivacic, C. / Pache, R.A. / Barlow, K.A. / Ollikainen, N. / Jeon, D. / Kelly, M.J.S. / Fraser, J.S. / Kortemme, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ob5.cif.gz | 374.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ob5.ent.gz | 307.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ob5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ob5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6ob5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ob5_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 6ob5_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/6ob5 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/6ob5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40825.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, SAMEA3485101_02947 / Variant: S3-2D / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Y0TBT9, UniProt: P0AEX9*PLUS #2: Protein | Mass: 17778.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: computationally-designed sequence / Source: (gene. exp.) unidentified (others) / Variant: S3-2D / Production host: Escherichia coli (E. coli) #3: Polysaccharide | #4: Chemical | ChemComp-FPP / | #5: 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: 2.12 Å3/Da / Density % sol: 41.86 % / Description: Thin, flat plates. Commonly stacked. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1M Tris Buffer, 0.1M sodium chloride, and 32% PEG-6000 PH range: 8.5-8.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2016 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→95.47 Å / Num. obs: 45972 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rpim(I) all: 0.033 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.3 / Num. unique obs: 7746 / CC1/2: 0.966 / Rpim(I) all: 0.09 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVX, 1FQD Resolution: 2.208→95.46 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 32.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.208→95.46 Å
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Refine LS restraints |
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LS refinement shell |
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