+Open data
-Basic information
Entry | Database: PDB / ID: 8hnf | ||||||
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Title | Crystal structure of the ancestral GH19 chitinase Anc5 | ||||||
Components | Anc5, ancestral GH19 chitinase | ||||||
Keywords | HYDROLASE / GH19 Chitinase | ||||||
Function / homology | Chem-1PG Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Kozome, D. / Laurino, P. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Emergence of antifungal activity in GH19 chitinases through gain-of-function in a remote loop. Authors: Kozome, D. / Laurino, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hnf.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hnf.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hnf_validation.pdf.gz | 951.1 KB | Display | wwPDB validaton report |
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Full document | 8hnf_full_validation.pdf.gz | 952.3 KB | Display | |
Data in XML | 8hnf_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8hnf_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/8hnf ftp://data.pdbj.org/pub/pdb/validation_reports/hn/8hnf | HTTPS FTP |
-Related structure data
Related structure data | 8hneC 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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Unit cell |
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-Components
#1: Protein | Mass: 26256.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-1PG / |
#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 Å3/Da / Density % sol: 38.36 % |
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Crystal grow | Temperature: 316 K / Method: vapor diffusion, hanging drop Details: 27% (w/v) polyethylene glycol monomethyl ether 2000, 0.1M MES monohydrate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→38.69 Å / Num. obs: 28613 / % possible obs: 99.54 % / Redundancy: 2 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.06581 / Net I/σ(I): 10.36 |
Reflection shell | Resolution: 1.57→1.627 Å / Rmerge(I) obs: 0.4842 / Num. unique obs: 2773 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→38.69 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8092 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 25.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→38.69 Å
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Refine LS restraints |
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LS refinement shell |
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