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Yorodumi- PDB-4cub: Unravelling the multiple functions of the architecturally intrica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cub | |||||||||
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Title | Unravelling the multiple functions of the architecturally intricate Streptococcus pneumoniae beta-galactosidase, BgaA | |||||||||
Components | BETA-GALACTOSIDASE | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Singh, A.K. / Pluvinage, B. / Higgins, M.A. / Dalia, A.B. / Flynn, M. / Lloyd, A.R. / Weiser, J.N. / Stubbs, K.A. / Boraston, A.B. / King, S.J. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Unravelling the Multiple Functions of the Architecturally Intricate Streptococcus Pneumoniae Beta-Galactosidase, Bgaa. Authors: Singh, A.K. / Pluvinage, B. / Higgins, M.A. / Dalia, A.B. / Woodiga, S.A. / Flynn, M. / Lloyd, A.R. / Weiser, J.N. / Stubbs, K.A. / Boraston, A.B. / King, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cub.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cub.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 4cub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cub_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4cub_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4cub_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4cub_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/4cub ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cub | HTTPS FTP |
-Related structure data
Related structure data | 4cu6C 4cu7C 4cu8C 4cu9C 4cuaC 4cucC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20164.234 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 1463-1645 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: NCH18 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8DQP4, beta-galactosidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.32 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97874 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97874 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 24686 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.62 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.809 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 mean: 21.984 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.62 Å
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Refine LS restraints |
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