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Yorodumi- PDB-5ac4: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ac4 | ||||||
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Title | GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with GalNAc | ||||||
Components | N-ACETYL-BETA-D-GLUCOSAMINIDASE | ||||||
Keywords | HYDROLASE / BACTERIAL PROTEINS / CARBOHYDRATE CONFORMATION / CATALYTIC DOMAIN / HOST-PATHOGEN INTERACTIONS / HYDROLYSIS / POLYSACCHARIDES / VIRULENCE FACTORS | ||||||
Function / homology | Function and homology information hexosaminidase activity / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Cid, M. / Robb, C.S. / Higgins, M.A. / Boraston, A.B. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2015 Title: A Second beta-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans. Authors: Robb, M. / Robb, C.S. / Higgins, M.A. / Hobbs, J.K. / Paton, J.C. / Boraston, A.B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ac4.cif.gz | 266 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ac4.ent.gz | 213.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ac4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5ac4 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5ac4 | HTTPS FTP |
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-Related structure data
Related structure data | 5a69C 5a6aC 5a6bC 5a6jC 5a6kC 5ac5C 2epnS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 74180.531 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C1CH75, UniProt: A0A0H2US73*PLUS, beta-N-acetylhexosaminidase #2: Sugar | #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: 2.19 Å3/Da / Density % sol: 43.94 % / Description: NONE |
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Crystal grow | pH: 10.2 Details: 12% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→79.54 Å / Num. obs: 74999 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EPN Resolution: 2.08→133.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.877 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.164 / 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: 17.666 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→133.45 Å
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Refine LS restraints |
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