+Open data
-Basic information
Entry | Database: PDB / ID: 6num | |||||||||||||||
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Title | The structure of GH32 from Bifidobacteium adolescentis | |||||||||||||||
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: 1.9 Å | |||||||||||||||
Authors | Lima, M.Z.T. / Muniz, J.R.C. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: To Be Published Title: The structure of GH32 from Bifidobacteium adolescentis 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 | 6num.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6num.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 6num.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/6num ftp://data.pdbj.org/pub/pdb/validation_reports/nu/6num | 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: 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: 2.23 Å3/Da / Density % sol: 44.9 % |
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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: 1.9→45.91 Å / Num. obs: 41542 / % possible obs: 99.8 % / Redundancy: 18.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.043 / Rrim(I) all: 0.137 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 17.3 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2636 / CC1/2: 0.968 / Rpim(I) all: 0.252 / Rrim(I) all: 0.79 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.378 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→38.378 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.8742 Å / Origin y: -10.2285 Å / Origin z: 4.3576 Å
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Refinement TLS group | Selection details: all |