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- PDB-6wxa: Crystal structure of truncated Streptococcal bacteriophage hyalur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wxa | ||||||
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Title | Crystal structure of truncated Streptococcal bacteriophage hyaluronidase complexed with unsaturated hyaluronan hexa-saccharides | ||||||
![]() | Hyaluronan lyase | ||||||
![]() | LYASE / HylP / Hyaluronidase / S. pyogenes phage H4489A / Beta-elimination / unsaturated Hyaluronan hexa-saccharides | ||||||
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 | ![]() | 323.2 KB | Display | ![]() |
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PDB format | ![]() | 266.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 43.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wv2SC ![]() 6wwxC ![]() 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
-Protein , 1 types, 3 molecules ABC
#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: ![]() ![]() |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 139 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-NI / |
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#6: Water | ChemComp-HOH / |
-Details
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: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% (v/v) 2-PROPANOL, 20% (w/v) PEG 4000, 0.1M HEPES PH 7.5; Addition of unsaturated Hyaluronan Hexa-saccharides 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: 2.3→50 Å / Num. obs: 44512 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.573 / Net I/av σ(I): 29 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4399 / Χ2: 1.345 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6WV2 Resolution: 2.3→44.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.233 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.33 / ESU R Free: 0.235 / 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: 140.4 Å2 / Biso mean: 52.3 Å2 / Biso min: 28.66 Å2
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Refinement step | Cycle: final / Resolution: 2.3→44.91 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: 2.3→2.38 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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