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Yorodumi- PDB-1n7q: Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A Double Mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n7q | |||||||||
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Title | Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A Double Mutant complex with hyaluronan hexasacchride | |||||||||
Components | HYALURONIDASE | |||||||||
Keywords | LYASE / protein mutant | |||||||||
Function / homology | Function and homology information hyaluronate lyase / hyaluronate lyase activity / cell wall / carbohydrate binding / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 1LOH / Resolution: 2.3 Å | |||||||||
Authors | Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The function of hydrophobic residues in the catalytic cleft of Streptococcus pneumoniae hyaluronate lyase. Kinetic characterization of mutant enzyme forms Authors: Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n7q.cif.gz | 166.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7q.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7q ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7q | 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: 82087.375 Da / Num. of mol.: 1 / Mutation: W291A/W292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET20 / Production host: Escherichia coli (E. coli) References: GenBank: 437705, UniProt: Q8CWU3*PLUS, hyaluronate lyase |
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#2: Polysaccharide | beta-D-galactopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-galactopyranuronic 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-(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: 2.5 Å3/Da / Density % sol: 50.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
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: 2.3→50 Å / Num. obs: 39739 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.175 / Rsym value: 0.175 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.836 / Rsym value: 0.836 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 39864 / Num. measured all: 211022 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: 1LOH / Resolution: 2.3→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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LS refinement shell | Resolution: 2.3→2.38 Å /
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.22 |