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Yorodumi- PDB-2dp5: Structure of streptococcus pyogenes bacteriophage-associated hyal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dp5 | ||||||
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Title | Structure of streptococcus pyogenes bacteriophage-associated hyaluronate lyase Hylp2 | ||||||
Components | Hyaluronidase | ||||||
Keywords | LYASE / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED BETA-HELIX / HYALURONIDASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.55 Å | ||||||
Authors | Mishra, P. / Bhakuni, V. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Structure of streptococcus pyogenes bacteriophage-associated hyaluronate lyase Hylp2 Authors: Mishra, P. / Bhakuni, V. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / 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 | 2dp5.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dp5.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dp5 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dp5 | 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: 35834.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: PET 21d / Gene (production host): hyl P2 / 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: 2.7 Å3/Da / Density % sol: 54.2 % |
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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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 6, 2006 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→20 Å / Num. all: 5360 / Num. obs: 5360 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.128 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.55→3.65 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.285 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C3F Resolution: 3.55→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.885 / SU B: 45.134 / SU ML: 0.718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.658 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.47 Å2
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Refinement step | Cycle: LAST / Resolution: 3.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.55→3.639 Å / Total num. of bins used: 20 /
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