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Yorodumi- PDB-5zn6: Crystal structure of GH31 alpha-xylosidase from a soil metagenome -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zn6 | ||||||
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Title | Crystal structure of GH31 alpha-xylosidase from a soil metagenome | ||||||
Components | Alpha-xylosidase MeXyl31 | ||||||
Keywords | HYDROLASE / Hydolase | ||||||
Biological species | soil metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Matsuzawa, T. / Nakamichi, Y. / Watanabe, M. / Yaoi, K. | ||||||
Citation | Journal: To Be Published Title: Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome Authors: Matsuzawa, T. / Nakamichi, Y. / Watanabe, M. / Yaoi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zn6.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5zn6.ent.gz | 951.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zn6_validation.pdf.gz | 502.4 KB | Display | wwPDB validaton report |
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Full document | 5zn6_full_validation.pdf.gz | 518.3 KB | Display | |
Data in XML | 5zn6_validation.xml.gz | 207.1 KB | Display | |
Data in CIF | 5zn6_validation.cif.gz | 305.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/5zn6 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/5zn6 | HTTPS FTP |
-Related 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: 78373.375 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) soil metagenome (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-GOL / #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: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.6 M lithium sulfate, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 561527 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 23616 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.894 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.11
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.26 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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