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Yorodumi- PDB-5xe5: Discovery and structural analysis of a phloretin hydrolase from t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xe5 | ||||||
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Title | Discovery and structural analysis of a phloretin hydrolase from the opportunistic pathogen Mycobacterium abscessus | ||||||
Components | phloretin hydrolase | ||||||
Keywords | HYDROLASE / phloretin hydrolase / Bet v1 fold / C-C bond / flavonoid | ||||||
Function / homology | phloretin hydrolase / phloretin hydrolase activity / DAPG hydrolase, PhiG domain / DAPG hydrolase PhiG domain / metal ion binding / Phloretin hydrolase Function and homology information | ||||||
Biological species | Mycobacterium abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | He, Y.X. / Han, J.T. / Jia, W.J. / Zhang, Z. | ||||||
Citation | Journal: FEBS J. / Year: 2019 Title: Discovery and structural analysis of a phloretin hydrolase from the opportunistic human pathogen Mycobacterium abscessus. Authors: Han, J.T. / Zhang, S.P. / Jia, W.J. / Zhang, Z. / Wang, Y. / He, Y.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xe5.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xe5.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xe5_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 5xe5_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 5xe5_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 5xe5_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xe5 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xe5 | HTTPS FTP |
-Related structure data
Related structure data | 5xeyC 3hwpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31937.455 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria) Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 Gene: MAB_4487c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MK49 #2: Chemical | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Na-cacodylate pH 5.0, 1 M LiCl, 6.8% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.17→50 Å / Num. obs: 34081 / % possible obs: 97.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Χ2: 0.851 / Net I/av σ(I): 12.737 / Net I/σ(I): 6.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HWP Resolution: 2.17→36.786 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.72 Å2 / Biso mean: 35.6812 Å2 / Biso min: 13.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→36.786 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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