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Yorodumi- PDB-5hon: Structure of Domain 4 of AbnA, a GH43 extracellular arabinanase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hon | |||||||||
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Title | Structure of Domain 4 of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus, in complex with arabinotriose | |||||||||
Components | Extracellular arabinanase | |||||||||
Keywords | HYDROLASE / GH43 / arabinanase / arabinotriose / Geobacillus stearothermophilus | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | |||||||||
Authors | Lansky, S. / Azoulai, D. / Shwartstien, O. / Shoham, Y. / Shoham, G. | |||||||||
Citation | Journal: To Be Published Title: Structure of Domain 4 of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus, in complex with arabinotriose Authors: Lansky, S. / Azoulai, D. / Shwartstien, O. / 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 | 5hon.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hon.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hon_validation.pdf.gz | 1020.3 KB | Display | wwPDB validaton report |
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Full document | 5hon_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5hon_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5hon_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/5hon ftp://data.pdbj.org/pub/pdb/validation_reports/ho/5hon | HTTPS FTP |
-Related structure data
Related structure data | 4ho0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22757.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: abnA / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYN2 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22-24.5% PEG 3350, 0.1M Bis-Tris pH 5.5-6 / PH range: 5.5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 24952 / % possible obs: 93.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.7 / % possible all: 65.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO0 Resolution: 2.001→37.749 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.87 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→37.749 Å
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Refine LS restraints |
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LS refinement shell |
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