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- PDB-5a6b: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a6b | ||||||
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Title | GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with PUGNAc | ||||||
![]() | (N-ACETYL-BETA-D-GLUCOSAMINIDASE) x 2 | ||||||
![]() | HYDROLASE / BETA-HEXOSAMINIDASE / STREPTOCOCCUS PNEUMONIAE / BACTERIAL PROTEINS / CARBOHYDRATE CONFORMATION / CATALYTIC DOMAIN / ENZYME INHIBITORS / HOST-PATHOGEN INTERACTIONS / HYDROGEN BONDING / HYDROLYSIS / MODELS / POLYSACCHARIDES / PROTEIN BINDING / VIRULENCE FACTORS | ||||||
Function / homology | ![]() hexosaminidase activity / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cid, M. / Robb, C.S. / Higgins, M.A. / Boraston, A.B. | ||||||
![]() | ![]() 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. 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. THE SHEETS PRESENTED AS "CB" 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. THE SHEETS PRESENTED AS "DB" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 527.2 KB | Display | ![]() |
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PDB format | ![]() | 427.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 101.6 KB | Display | |
Data in CIF | ![]() | 152.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a69C ![]() 5a6aC ![]() 5a6jC ![]() 5a6kC ![]() 5ac4C ![]() 5ac5C ![]() 2epnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 74130.453 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 74017.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-OAN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % / 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→38.66 Å / Num. obs: 248507 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.9 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2EPN Resolution: 1.77→38.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.394 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.11 / 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: 24.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→38.69 Å
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Refine LS restraints |
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