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Yorodumi- PDB-4o8n: Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o8n | ||||||
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Title | Crystal structure of SthAraf62A, a GH62 family alpha-L-arabinofuranosidase from Streptomyces thermoviolaceus, in the apoprotein form | ||||||
Components | Alpha-L-arabinofuranosidase | ||||||
Keywords | HYDROLASE / 5-fold beta-propeller / glycosyl hydrolase family 62 / GH62 / alpha-L-arabinofuranosidase | ||||||
Function / homology | Function and homology information L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces thermoviolaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6476 Å | ||||||
Authors | Stogios, P.J. / Wang, W. / Xu, X. / Cui, H. / Master, E. / Savchenko, A. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2014 Title: Elucidation of the molecular basis for arabinoxylan-debranching activity of a thermostable family GH62 alpha-l-arabinofuranosidase from Streptomyces thermoviolaceus. Authors: Wang, W. / Mai-Gisondi, G. / Stogios, P.J. / Kaur, A. / Xu, X. / Cui, H. / Turunen, O. / Savchenko, A. / Master, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o8n.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o8n.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/4o8n ftp://data.pdbj.org/pub/pdb/validation_reports/o8/4o8n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42096.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces thermoviolaceus (bacteria) Gene: stxIV / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76BV4 |
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-Non-polymers , 5 types, 544 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-BTB / |
#4: Chemical | ChemComp-P6G / |
#5: Chemical | ChemComp-PEG / |
#6: 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: 1.98 Å3/Da / Density % sol: 37.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18 mg/mL SthAraf62A, 0.1 M Bis-tris propane pH 6.5, 20% PEG 5K MME, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 29, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6476→25 Å / Num. obs: 39537 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.9 % / Rsym value: 0.081 / Net I/σ(I): 29.96 |
Reflection shell | Resolution: 1.6476→1.68 Å / Redundancy: 92.7 % / Mean I/σ(I) obs: 4 / Num. unique all: 1895 / Rsym value: 0.587 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6476→24.452 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.66 / Stereochemistry target values: ML
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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: 1.6476→24.452 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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