+Open data
-Basic information
Entry | Database: PDB / ID: 7eyo | |||||||||||||||
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Title | Crystal structure of leech hyaluronidase | |||||||||||||||
Components | Hyaluronoglucuronidase | |||||||||||||||
Keywords | HYDROLASE / Hyaluronidae / GH79 | |||||||||||||||
Function / homology | hyaluronoglucuronidase / hyaluronoglucuronidase activity / Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / hyaluronan catabolic process / transferase activity / Glycoside hydrolase superfamily / membrane / Hyaluronoglucuronidase Function and homology information | |||||||||||||||
Biological species | Hirudo nipponia (invertebrata) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||||||||
Authors | Huang, H. / Hou, X.D. / Rao, Y.J. / Kang, Z. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Carbohydr Polym / Year: 2022 Title: Structure and cleavage pattern of a hyaluronate 3-glycanohydrolase in the glycoside hydrolase 79 family. Authors: Huang, H. / Hou, X. / Xu, R. / Deng, Z. / Wang, Y. / Du, G. / Rao, Y. / Chen, J. / Kang, Z. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eyo.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eyo.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 7eyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eyo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7eyo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7eyo_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7eyo_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/7eyo ftp://data.pdbj.org/pub/pdb/validation_reports/ey/7eyo | HTTPS FTP |
-Related structure data
Related structure data | 5la4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56122.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo nipponia (invertebrata) / Production host: Komagataella pastoris (fungus) / References: UniProt: X4Y2L4, hyaluronoglucuronidase | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: trisodium citrate, ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 43983 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.912 / Net I/σ(I): 9.2 / Num. measured all: 295605 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LA4 Resolution: 1.85→43.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.049 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.03 Å2 / Biso mean: 23.858 Å2 / Biso min: 6.46 Å2
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Refinement step | Cycle: final / Resolution: 1.85→43.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.896 Å / Rfactor Rfree error: 0
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