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Yorodumi- PDB-2wb3: The partial structure of a group A streptococcal phage-encoded ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wb3 | ||||||
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Title | The partial structure of a group A streptococcal phage-encoded tail fibre hyaluronate lyase Hylp3 | ||||||
Components | HYALURONIDASE-PHAGE ASSOCIATED | ||||||
Keywords | LYASE / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED BETA- HELIX / HYALURONIDASE / SCARLET FEVER | ||||||
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: 1.9 Å | ||||||
Authors | Martinez-Fleites, C. / Black, G.W. / Turkenburg, J.P. / Smith, N.L. / Taylor, E.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structures of Two Truncated Phage-Tail Hyaluronate Lyases from Streptococcus Pyogenes Serotype M1. Authors: Martinez-Fleites, C. / Smith, N.L. / Turkenburg, J.P. / Black, G.W. / Taylor, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wb3.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wb3.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wb3 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wb3 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16854.125 Da / Num. of mol.: 1 / Fragment: HYALURONATE LYASE FRAGMENT, RESIDUES 214-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS SF370 / Plasmid: PET28A (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99Z19, hyaluronate lyase |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS STRUCTURE IS A FRAGMENT, THE N-TERMINAL PORTION IS MISSING, THE STRUCTURE BEGINS AT RESIDUE 234. |
-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: 51 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.5, 30 % (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 13481 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / % possible all: 51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.385 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 33.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.58 Å
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Refine LS restraints |
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