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Yorodumi- PDB-1n7r: Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A/F343V Muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n7r | |||||||||
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Title | Streptococcus pneumoniae Hyaluronate Lyase W291A/W292A/F343V Mutant complex with hexasaccharide hyaluronan | |||||||||
Components | HYALURONIDASE | |||||||||
Keywords | LYASE / protein mutant | |||||||||
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: 2.2 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 | 1n7r.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7r.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7r ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7r | HTTPS FTP |
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-Related structure data
Related structure data | 1n7nC 1n7oC 1n7pC 1n7qC 1lohS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 82039.328 Da / Num. of mol.: 1 / Mutation: W291A/W292A/F343V 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: 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-(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: 2.53 Å3/Da / Density % sol: 51.05 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
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 / Date: Jul 21, 2002 / Details: SI |
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: 2.2→50 Å / Num. obs: 45691 / % possible obs: 99.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.206 / Rsym value: 0.206 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.421 / Rsym value: 0.421 |
Reflection | *PLUS Highest resolution: 2.21 Å / Lowest resolution: 50 Å / Num. obs: 45837 / Num. measured all: 394836 |
Reflection shell | *PLUS % possible obs: 98.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LOH Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refinement | *PLUS Highest resolution: 2.21 Å / Lowest resolution: 50 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.204 |