+Open data
-Basic information
Entry | Database: PDB / ID: 5swi | ||||||
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Title | Crystal structure of SpGH92 in complex with mannose | ||||||
Components | Sugar hydrolase | ||||||
Keywords | HYDROLASE / Beta sandwich / (alpha/alpha)6 barrel / glycoside hydrolase | ||||||
Function / homology | Function and homology information carbohydrate binding / hydrolase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Shapiro-Ward, S. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: PLoS Pathog. / Year: 2017 Title: Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence. Authors: Robb, M. / Hobbs, J.K. / Woodiga, S.A. / Shapiro-Ward, S. / Suits, M.D. / McGregor, N. / Brumer, H. / Yesilkaya, H. / King, S.J. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5swi.cif.gz | 578.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5swi.ent.gz | 466.8 KB | Display | PDB format |
PDBx/mmJSON format | 5swi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5swi ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5swi | HTTPS FTP |
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-Related structure data
Related structure data | 5suoC 5swaC 5swbC 2wvyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 81576.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: ERS003549_00384, ERS409165_00851, ERS409372_00266, ERS455085_01031, ERS515225_01644 Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0Y0HIE3 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Sugar | ChemComp-BMA / #5: 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: 3.47 Å3/Da / Density % sol: 64.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.25 M (NH4)2SO4, 0.1M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97531 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97531 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→127.76 Å / Num. obs: 237386 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WVY Resolution: 2.15→127.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.1722 / FOM work R set: 0.8167 / SU B: 5.311 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1821 / SU Rfree: 0.1563 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 100.57 Å2 / Biso mean: 35.789 Å2 / Biso min: 13.76 Å2
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Refinement step | Cycle: final / Resolution: 2.15→127.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.151→2.207 Å / Total num. of bins used: 20
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