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Yorodumi- PDB-8g0o: Crystal structure of Y281F mutant of Hyaluronate lyase B from Cut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g0o | ||||||
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Title | Crystal structure of Y281F mutant of Hyaluronate lyase B from Cutibacterium acnes | ||||||
Components | Hyaluronate lyase | ||||||
Keywords | LYASE / Polysaccharide lyase / Glycosaminoglycan (GAG) lyase / Hyaluronate lyase / Inflammation | ||||||
Function / homology | Function and homology information hyaluronate lyase / hyaluronate lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Cutibacterium acnes HL110PA3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Katiki, M. / McNally, R. / Chatterjee, A. / Hajam, I.A. / Liu, G.Y. / Murali, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Functional divergence of a bacterial enzyme promotes healthy or acneic skin. Authors: Hajam, I.A. / Katiki, M. / McNally, R. / Lazaro-Diez, M. / Kolar, S. / Chatterjee, A. / Gonzalez, C. / Paulchakrabarti, M. / Choudhury, B. / Caldera, J.R. / Desmond, T. / Tsai, C.M. / Du, X. ...Authors: Hajam, I.A. / Katiki, M. / McNally, R. / Lazaro-Diez, M. / Kolar, S. / Chatterjee, A. / Gonzalez, C. / Paulchakrabarti, M. / Choudhury, B. / Caldera, J.R. / Desmond, T. / Tsai, C.M. / Du, X. / Li, H. / Murali, R. / Liu, G.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g0o.cif.gz | 310.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g0o.ent.gz | 245.9 KB | Display | PDB format |
PDBx/mmJSON format | 8g0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g0o_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 8g0o_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 8g0o_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 8g0o_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0o ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0o | HTTPS FTP |
-Related structure data
Related structure data | 8fnxC 8fygC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 83462.992 Da / Num. of mol.: 2 / Mutation: Y281F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cutibacterium acnes HL110PA3 (bacteria) Strain: HL110PA3 / Gene: PPA0380 / Plasmid: pET / Details (production host): pET His6 TEV LIC cloning vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CZ01, hyaluronate lyase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M bis-tris pH 6.5, 0.4 M MgCl2, 16% PEG 3350, and 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2018 |
Radiation | Monochromator: MSC/Yale double focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.72 Å / Num. obs: 85175 / % possible obs: 92.5 % / Redundancy: 1.9 % / CC1/2: 0.981 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.12 / Rrim(I) all: 0.17 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.548 / Num. unique obs: 11885 / CC1/2: 0.853 / Rpim(I) all: 0.548 / Rrim(I) all: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.72 Å / Cross valid method: FREE R-VALUE / σ(F): 16.43 / Phase error: 42.47 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.72 Å
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Refine LS restraints |
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LS refinement shell |
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