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Yorodumi- PDB-4cu7: Unravelling the multiple functions of the architecturally intrica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cu7 | ||||||
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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 / carbohydrate catabolic process / beta-galactosidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AJ" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AJ" 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 | 4cu7.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cu7.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cu7_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
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Full document | 4cu7_full_validation.pdf.gz | 487.3 KB | Display | |
Data in XML | 4cu7_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 4cu7_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/4cu7 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cu7 | HTTPS FTP |
-Related structure data
Related structure data | 4cu6C 4cu8C 4cu9C 4cuaC 4cubC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 96325.125 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 137-985 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: I6L8R4, UniProt: A0A0H2UP19*PLUS, beta-galactosidase | ||||
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#2: Chemical | ChemComp-GIF / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.36 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 |
Detector | Type: MARRESEARCH / 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: 2.2→38.93 Å / Num. obs: 77385 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.7 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→116.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.293 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.136 / 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: 21.324 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→116.78 Å
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Refine LS restraints |
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