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- PDB-6wwx: Crystal structure of truncated bacteriophage hyaluronan lyase Hyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wwx | ||||||
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Title | Crystal structure of truncated bacteriophage hyaluronan lyase HylP in complex with unsaturated hyaluronan tetra-saccharides | ||||||
![]() | Hyaluronoglucosaminidase | ||||||
![]() | LYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination | ||||||
Function / homology | ![]() symbiont entry into host cell via disruption of host cell glycocalyx / hyaluronoglucosaminidase / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / symbiont entry into host cell via disruption of host cell envelope / virion component Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deivanayagam, C. / Schormann, N. | ||||||
![]() | ![]() Title: Crystal Structure of Streptococcal Bacteriophage Hyaluronidase: Presence of a Prokaryotic Collagen and Elucidation of Catalytic Mechanism Authors: Lee, J.H. / Schormann, N. / Rajashankar, K.R. / Deivanaygam, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323 KB | Display | ![]() |
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PDB format | ![]() | 265.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wv2SC ![]() 6wxaC ![]() 6x3mC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 31532.449 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HYLP1, HYLP / Plasmid: pET24a / Production host: ![]() ![]() #2: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic 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: Chemical | ChemComp-NI / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% (v/v) 2-Propanol, 20% (w/v) PEG 4000, 0.1 M Hepes, pH 7.5; incubation of protein HylP with unsaturated Hyaluronan tetra-saccharides at 1:20 molar ratio prior to crystallization |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 51169 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.325 / Net I/av σ(I): 30.4 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 5022 / Χ2: 1.185 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WV2 Resolution: 2.2→38.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.337 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.38 Å2 / Biso mean: 44.9 Å2 / Biso min: 23.55 Å2
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Refinement step | Cycle: final / Resolution: 2.2→38.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.2→2.26 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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