+Open data
-Basic information
Entry | Database: PDB / ID: 8ip1 | ||||||
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Title | Escherichia coli OpgD mutant-D388N with beta-1,2-glucan | ||||||
Components | Glucans biosynthesis protein D | ||||||
Keywords | HYDROLASE / Beta-1 / 2-glucanase | ||||||
Function / homology | Function and homology information beta-glucan biosynthetic process / glucan biosynthetic process / catalytic activity / outer membrane-bounded periplasmic space / carbohydrate binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Motouchi, S. / Nakajima, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Identification of enzymatic functions of osmo-regulated periplasmic glucan biosynthesis proteins from Escherichia coli reveals a novel glycoside hydrolase family. Authors: Motouchi, S. / Kobayashi, K. / Nakai, H. / Nakajima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ip1.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ip1.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ip1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/8ip1 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/8ip1 | HTTPS FTP |
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-Related structure data
Related structure data | 8ioxC 8ip2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63899.949 Da / Num. of mol.: 2 / Mutation: D388N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: opgD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40120 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose Type: oligosaccharide / Mass: 1801.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose Type: oligosaccharide / Mass: 2125.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 569 molecules
#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-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: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MMT (pH 4.0), PEG1500, Beta-1,2-glucan |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→47.74 Å / Num. obs: 66585 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.06→2.11 Å / Num. unique obs: 4130 / CC1/2: 0.697 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→47.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.155 / Average fsc free: 0.9129 / Average fsc work: 0.9237 / Cross valid method: FREE R-VALUE / ESU R: 0.211 / ESU R Free: 0.177 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.845 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→47.74 Å
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Refine LS restraints |
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LS refinement shell |
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