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Yorodumi- PDB-6s00: Crystal structure of an inverting family GH156 exosialidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s00 | ||||||
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Title | Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-acetylneuraminic acid | ||||||
Components | exosialidase from uncultured bacterium pG7 | ||||||
Keywords | HYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer | ||||||
Function / homology | N-acetyl-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 | 6s00.cif.gz | 406 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s00.ent.gz | 333.3 KB | Display | PDB format |
PDBx/mmJSON format | 6s00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s00_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6s00_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6s00_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6s00_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s00 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s00 | HTTPS FTP |
-Related structure data
Related structure data | 6rzdSC 6s04C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 6 - 502 / Label seq-ID: 6 - 502
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-Components
#1: Protein | Mass: 58786.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium pG7 (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) / References: exo-alpha-sialidase #2: Chemical | ChemComp-GOL / #3: Sugar | #4: Chemical | ChemComp-PG4 / | #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: 2.43 Å3/Da / Density % sol: 49.38 % |
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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: 1.7001 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7001 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→49.75 Å / Num. obs: 76209 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 0.993 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.071 / Rrim(I) all: 0.302 / Net I/σ(I): 10.3 / Num. measured all: 1371172 / Scaling rejects: 114 | ||||||||||||||||||||||||
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→49.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.647 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.177 / 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: 63.32 Å2 / Biso mean: 23.084 Å2 / Biso min: 7.83 Å2
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Refinement step | Cycle: final / Resolution: 2→49.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 17057 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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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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