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Yorodumi- PDB-4qjy: Crystal structure of native Ara127N, a GH127 beta-L-arabinofurano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qjy | ||||||
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Title | Crystal structure of native Ara127N, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6 | ||||||
Components | GH127 beta-L-arabinofuranosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.294 Å | ||||||
Authors | Lansky, S. / Salama, R. / Dann, R. / Shner, I. / Manjasetty, B. / Belrhali, H. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To be Published Title: Crystal structure of native Ara127N, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6 Authors: Lansky, S. / Salama, R. / Dann, R. / Shner, I. / Manjasetty, B. / Belrhali, H. / 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 | 4qjy.cif.gz | 273.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qjy.ent.gz | 227.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qjy_validation.pdf.gz | 318.6 KB | Display | wwPDB validaton report |
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Full document | 4qjy_full_validation.pdf.gz | 334.7 KB | Display | |
Data in XML | 4qjy_validation.xml.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qjy ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjy | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 74558.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T6 / Gene: araN / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYN9 #2: Chemical | ChemComp-ACT / #3: 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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG300, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.294→30 Å / Num. all: 58582 / Num. obs: 58318 / % possible obs: 99.55 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.294→2.34 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.294→29.89 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.946 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.294→29.89 Å
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Refine LS restraints |
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