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Yorodumi- PDB-1f9g: CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f9g | ||||||
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Title | CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE COCRYSTALLIZED WITH ASCORBIC ACID | ||||||
Components | HYALURONATE LYASE | ||||||
Keywords | LYASE / Ascorbic acid binds to the indole group of Trp292 / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information hyaluronate lyase / hyaluronate lyase activity / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Li, S. / Jedrzejas, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Vitamin C inhibits the enzymatic activity of Streptococcus pneumoniae hyaluronate lyase. Authors: Li, S. / Taylor, K.B. / Kelly, S.J. / Jedrzejas, M.J. #1: Journal: Embo J. / Year: 2000 Title: Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase Authors: Jedrzejas, M.J. #2: Journal: J.Mol.Biol. / Year: 2000 Title: Mechanism of hyaluronan binding and degradation: Structure of Streptococcus pneumoniae hyaluronate lyase in complex with hyaluronic acid disaccharide at 1.7 angstrom resolution Authors: Jedraejas, M.J. #3: Journal: To be Published / Year: 2000 Title: Crystal structure, enzymatic mechanism and action pattern of Streptococcus agalactiae hyaluronate lyase, comparison with other bacterial polysaccharide lyases Authors: Jedraejas, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9g.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9g.ent.gz | 125.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f9g_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 1f9g_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 1f9g_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1f9g_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9g ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9g | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is a monomer in one assymetry unit. |
-Components
#1: Protein | Mass: 83561.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54873, hyaluronate lyase |
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#2: Sugar | ChemComp-ASC / |
#3: 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: 2.67 Å3/Da / Density % sol: 53.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, sodium cacodylate, dioxane, sodium chloride, ascorbic acid , pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 10-100 mM / Common name: ascorbic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Feb 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 60317 / Num. obs: 54324 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.32 / Num. unique all: 1785 / % possible all: 60.1 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 60 % |
-Processing
Software |
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Refinement | Resolution: 2→45 Å / σ(F): 0.001 / σ(I): 0.001 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 2→45 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 45 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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