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Yorodumi- PDB-8fyg: Crystal structure of Hyaluronate lyase A from Cutibacterium acnes -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fyg | ||||||
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Title | Crystal structure of Hyaluronate lyase A from Cutibacterium acnes | ||||||
Components | Hyaluronate lyase | ||||||
Keywords | LYASE / Polysaccharide lyase / Glycosaminoglycan (GAG) lyase / Hyaluronate lyase / Inflammation | ||||||
Function / homology | Function and homology information hyaluronate lyase / carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region Similarity search - Function | ||||||
Biological species | Cutibacterium acnes HL043PA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 8fyg.cif.gz | 327.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fyg.ent.gz | 257.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fyg_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 8fyg_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 8fyg_validation.xml.gz | 65.2 KB | Display | |
Data in CIF | 8fyg_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/8fyg ftp://data.pdbj.org/pub/pdb/validation_reports/fy/8fyg | HTTPS FTP |
-Related structure data
Related structure data | 8fnxC 8g0oC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 83620.062 Da / Num. of mol.: 2 / Mutation: Y285F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cutibacterium acnes HL043PA1 (bacteria) Strain: HL043PA1 / Gene: HMPREF9570_01449 / Plasmid: pET Details (production host): pET His6 MBP TEV LIC cloning vector Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A828SH59, hyaluronate lyase #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na dihydrogen phosphate pH 6.5, 9% PEG 8000, 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: Feb 20, 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: 2.05→19.8 Å / Num. obs: 88266 / % possible obs: 93.9 % / Redundancy: 2.2 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.128 / Net I/σ(I): 7.33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.8 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→19.8 Å
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Refine LS restraints |
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LS refinement shell |
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