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Yorodumi- PDB-2yx2: Crystal structure of cloned trimeric hyluranidase from streptococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yx2 | ||||||
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Title | Crystal structure of cloned trimeric hyluranidase from streptococcus pyogenes at 2.8 A resolution | ||||||
Components | Hyaluronidase, phage associated | ||||||
Keywords | LYASE / hyluranidase / hyluronan lyase | ||||||
Function / homology | Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / Hyaluronidase, phage associated Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mishra, P. / Prem Kumar, R. / Bhakuni, V. / Singh, N. / Sharma, S. / Kaur, P. / Perbandt, M. / Betzel, C. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of cloned trimeric hyluranidase from streptococcus pyogenes at 2.8 A resolution Authors: Mishra, P. / Prem Kumar, R. / Bhakuni, V. / Singh, N. / Sharma, S. / Kaur, P. / Perbandt, M. / Betzel, C. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yx2.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yx2.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yx2 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yx2 | HTTPS FTP |
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-Related structure data
Related structure data | 2c3fS 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: 36468.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: HYL P2 / Plasmid: PET 21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0M7, hyaluronate lyase |
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#2: 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: 53.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: TRIS HCL, SODIUM FORMATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2006 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 10238 / Num. obs: 10238 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.058 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.8→2.84 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.308 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C3F Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.163 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.155 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.798→2.87 Å / Total num. of bins used: 20
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