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Yorodumi- PDB-1lxk: Streptococcus pneumoniae Hyaluronate Lyase in Complex with Tetras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lxk | |||||||||
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Title | Streptococcus pneumoniae Hyaluronate Lyase in Complex with Tetrasaccharide Hyaluronan Substrate | |||||||||
Components | Hyaluronate Lyase | |||||||||
Keywords | LYASE / PROTEIN-CARBOHYDRATE COMPLEX | |||||||||
Function / homology | Function and homology information hyaluronate lyase / hyaluronate lyase activity / organic substance catabolic process / 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 / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
Authors | Jedrzejas, M.J. / Mello, L.V. / De Groot, B.L. / Li, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. Authors: Jedrzejas, M.J. / Mello, L.V. / de Groot, B.L. / Li, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lxk.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lxk.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxk ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxk | HTTPS FTP |
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-Related 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: 82301.641 Da / Num. of mol.: 1 / Mutation: Y408F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 437705, UniProt: Q54873*PLUS, hyaluronate lyase |
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#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 2.68 Å3/Da / Density % sol: 54.03 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, SODIUM Cacodylate, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 |
Detector | Type: OXFORD / Detector: CCD / Date: Mar 20, 2001 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 124799 / % possible obs: 93.1 % |
Reflection shell | Resolution: 1.53→1.58 Å / % possible all: 49.8 |
Reflection | *PLUS Highest resolution: 1.52 Å / Lowest resolution: 50 Å / Num. obs: 124927 / Num. measured all: 904361 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Highest resolution: 1.52 Å / Lowest resolution: 1.59 Å / % possible obs: 49.8 % / Rmerge(I) obs: 0.611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.53→20 Å
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Refinement | *PLUS Highest resolution: 1.52 Å / Lowest resolution: 50 Å / % reflection Rfree: 1 % / Rfactor Rwork: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.52 Å / Lowest resolution: 1.59 Å / Rfactor Rfree: 0.395 / Rfactor Rwork: 0.33 |