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Yorodumi- PDB-2jka: Native structure of a family 97 alpha-glucosidase from Bacteroide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jka | ||||||
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Title | Native structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron | ||||||
Components | ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB) | ||||||
Keywords | HYDROLASE / FAMILY 97 / ALPHA-GLUCOSIDASE / GLYCOSIDE HYDROLASE / BACTEROIDES THETAIOTAOMICRON | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-glucosidase / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / starch catabolic process / carbohydrate binding / periplasmic space / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Gloster, T.M. / Turkenburg, J.P. / Potts, J.R. / Henrissat, B. / Davies, G.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Divergence of Catalytic Mechanism within a Glycosidase Family Provides Insight Into Evolution of Carbohydrate Metabolism by Human Gut Flora. Authors: Gloster, T.M. / Turkenburg, J.P. / Potts, J.R. / Henrissat, B. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jka.cif.gz | 329.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jka.ent.gz | 264.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jka_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 2jka_full_validation.pdf.gz | 469.5 KB | Display | |
Data in XML | 2jka_validation.xml.gz | 67.8 KB | Display | |
Data in CIF | 2jka_validation.cif.gz | 104.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/2jka ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jka | HTTPS FTP |
-Related 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: 83307.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P71094, UniProt: G8JZS4*PLUS, alpha-glucosidase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THE FIRST 21 RESIDUES OF THE GENE CORRESPOND TO A SIGNAL PEPTIDE SEQUENCE AND WERE NOT CLONED INTO ...THE FIRST 21 RESIDUES OF THE GENE CORRESPOND | |
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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Details: 18-22% POLYETHYLENE GLYCOL 3350, 0.02 M SODIUM/POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 23, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 120776 / % possible obs: 91.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.3 / % possible all: 56.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→14.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.04 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→14.94 Å
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Refine LS restraints |
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