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Yorodumi- PDB-6nun: Structure of GH32 hydrolase from Bifidobacterium adolescentis in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nun | |||||||||||||||
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Title | Structure of GH32 hydrolase from Bifidobacterium adolescentis in complex with frutose | |||||||||||||||
Components | Beta-fructofuranosidaseSucrase | |||||||||||||||
Keywords | HYDROLASE / GH32 / glycoside hydrolase | |||||||||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | |||||||||||||||
Biological species | Bifidobacterium adolescentis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||||||||
Authors | Lima, M.Z.T. / Muniz, J.R.C. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: To Be Published Title: Structure of GH32 from Bifidobacterium adolescentis in complex with fructose Authors: Lima, M.Z.T. / Muniz, J.R.C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nun.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nun.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/6nun ftp://data.pdbj.org/pub/pdb/validation_reports/nu/6nun | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58188.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium adolescentis (bacteria) Gene: B0703_1339 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X2ZCY9, UniProt: A1A2J8*PLUS | ||||
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#2: Chemical | ChemComp-EDO / #3: Sugar | ChemComp-FRU / | #4: 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: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M LiCl, 0.1 MMES pH 6.0, 20% (m/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→45.82 Å / Num. obs: 42137 / % possible obs: 99.5 % / Redundancy: 20.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.042 / Rrim(I) all: 0.141 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.87→1.91 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2604 / CC1/2: 0.838 / Rpim(I) all: 0.358 / Rrim(I) all: 1.11 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→45.82 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.721 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.429 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→45.82 Å
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Refine LS restraints |
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