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Yorodumi- PDB-6f1g: The structure of AbnB-E201A, an intracellular 1,5-alpha-L-arabina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f1g | |||||||||
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Title | The structure of AbnB-E201A, an intracellular 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus, in complex with arabinopentaose | |||||||||
Components | Intracellular endo-alpha-(1->5)-L-arabinanase | |||||||||
Keywords | HYDROLASE / arabinopentaose / geobacillus stearothermophilus / intracellular arabinanase / gh43 / glycoside hydrolase | |||||||||
Function / homology | Function and homology information arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.672 Å | |||||||||
Authors | Lansky, S. / Shwartshtien, O. / Salama, R. / Shoham, Y. / Shoham, G. | |||||||||
Citation | Journal: To Be Published Title: The structure of AbnB-E201A, an intracellular 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus, in complex with arabinopentaose Authors: Lansky, S. / Shwartshtien, O. / Salama, R. / Shoham, Y. / Shoham, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f1g.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1g.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 6f1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1g ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1g | HTTPS FTP |
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-Related structure data
Related structure data | 3d5yS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35676.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: abnB / Production host: Escherichia coli (E. coli) References: UniProt: B3EYM8, arabinan endo-1,5-alpha-L-arabinanase | ||
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#2: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | #5: 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: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.9-2.1 M LiSO4, 0.1 M Tris pH 8.5, 3% PEG400, 5mM arabinopentose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→30 Å / Num. obs: 34562 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1699 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D5Y Resolution: 1.672→29.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.672→29.73 Å
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Refine LS restraints |
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LS refinement shell |
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