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Yorodumi- PDB-5z6c: Crystal structure of Bacillus subtilis sugar-binding protein YesO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z6c | ||||||
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Title | Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan | ||||||
Components | Putative ABC transporter substrate-binding protein YesO | ||||||
Keywords | TRANSPORT PROTEIN / ABC transporter substrate-binding protein / sugar transport | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Putative ABC transporter substrate-binding protein YesO Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Sugiura, H. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan Authors: Sugiura, H. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z6c.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z6c.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z6c ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z6c | HTTPS FTP |
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-Related structure data
Related structure data | 4r6kS 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: 48390.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: yesO, BSU06970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31518 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.61 Å3/Da / Density % sol: 23.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MIB (sodium malonate, imidazole, boric acid) buffer (pH 6.0), 25% (w/v) PEG-1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 42265 / % possible obs: 98.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.06 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R6K Resolution: 1.97→37.261 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 26.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→37.261 Å
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Refine LS restraints |
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LS refinement shell |
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