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Yorodumi- PDB-8fxu: Thermoanaerobacter thermosaccharolyticum periplasmic Glucose-Bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fxu | ||||||
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Title | Thermoanaerobacter thermosaccharolyticum periplasmic Glucose-Binding Protein glucose complex: Badan conjugate attached at F17C | ||||||
Components | D-galactose/methyl-galactoside binding periplasmic protein MglB | ||||||
Keywords | SUGAR BINDING PROTEIN / Periplasmic binding protein / Biosensor Fluorescent conjugate | ||||||
Function / homology | beta-D-glucopyranose / : / Chem-YDQ Function and homology information | ||||||
Biological species | Thermoanaerobacterium thermosaccharolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Allert, M.J. / Kumar, S. / Beese, L.S. / Hellinga, H.W. | ||||||
Funding support | 1items
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Citation | Journal: Commun Chem / Year: 2023 Title: Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Authors: Allert, M.J. / Kumar, S. / Wang, Y. / Beese, L.S. / Hellinga, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fxu.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fxu.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fxu_validation.pdf.gz | 692.5 KB | Display | wwPDB validaton report |
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Full document | 8fxu_full_validation.pdf.gz | 692.6 KB | Display | |
Data in XML | 8fxu_validation.xml.gz | 17 KB | Display | |
Data in CIF | 8fxu_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/8fxu ftp://data.pdbj.org/pub/pdb/validation_reports/fx/8fxu | HTTPS FTP |
-Related structure data
Related structure data | 8fxtC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.5061/dryad.msbcc2g2x / Data set type: other data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 34276.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (bacteria) Gene: Thert_00913 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#2: Sugar | ChemComp-BGC / |
-Non-polymers , 5 types, 395 molecules
#3: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-K / | ||
#5: Chemical | ChemComp-YDQ / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 0.2 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→37.66 Å / Num. obs: 44519 / % possible obs: 99.83 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.08522 / Rpim(I) all: 0.034 / Net I/σ(I): 16.44 |
Reflection shell | Resolution: 1.59→1.647 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.7435 / Num. unique obs: 4304 / Rpim(I) all: 0.2944 / % possible all: 98.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→37.66 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.3857 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→37.66 Å
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Refine LS restraints |
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LS refinement shell |
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