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Yorodumi- PDB-6s04: Crystal structure of an inverting family GH156 exosialidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s04 | |||||||||
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Title | Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-glycolylneuraminic acid | |||||||||
Components | exosialidase from uncultured bacterium pG7 | |||||||||
Keywords | HYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer | |||||||||
Function / homology | ACETATE ION / N-glycolyl-beta-neuraminic acid Function and homology information | |||||||||
Biological species | uncultured bacterium pG7 (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Bule, P. / Blagova, E. / Chuzel, L. / Taron, C.H. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Authors: Bule, P. / Chuzel, L. / Blagova, E. / Wu, L. / Gray, M.A. / Henrissat, B. / Rapp, E. / Bertozzi, C.R. / Taron, C.H. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s04.cif.gz | 411 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s04.ent.gz | 337.8 KB | Display | PDB format |
PDBx/mmJSON format | 6s04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s04_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6s04_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6s04_validation.xml.gz | 42 KB | Display | |
Data in CIF | 6s04_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s04 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s04 | HTTPS FTP |
-Related structure data
Related structure data | 6rzdSC 6s00C 6s0eC 6s0fC S: Starting model for refinement C: citing same article (ref.) |
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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: 59349.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium pG7 (environmental samples) Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: exo-alpha-sialidase #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.49 Å3/Da / Density % sol: 50.58 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.8 M sodium formate, 12% PEG 4000, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→65.07 Å / Num. obs: 78077 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.963 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.126 / Rrim(I) all: 0.269 / Net I/σ(I): 3.7 / Num. measured all: 323640 / Scaling rejects: 570 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RZD Resolution: 2→64.89 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.863 / SU B: 11.843 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 46.46 Å2 / Biso mean: 17.122 Å2 / Biso min: 1.38 Å2
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Refinement step | Cycle: final / Resolution: 2→64.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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