+Open data
-Basic information
Entry | Database: PDB / ID: 1n7n | ||||||
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Title | Streptococcus pneumoniae Hyaluronate Lyase W292A Mutant | ||||||
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: 1.55 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 | 1n7n.cif.gz | 172.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7n.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7n ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7n | HTTPS FTP |
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-Related structure data
Related structure data | 1n7oC 1n7pC 1n7qC 1n7rC 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: 82202.508 Da / Num. of mol.: 1 / Mutation: W292A mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54873, hyaluronate lyase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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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 / Date: Jan 10, 2002 |
Radiation | Monochromator: SI crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 125637 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.807 / % possible all: 87.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 125839 / Num. measured all: 636169 |
Reflection shell | *PLUS % possible obs: 87.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LOH Resolution: 1.55→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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LS refinement shell | Resolution: 1.55→1.61 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 1 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.28 |