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Yorodumi- PDB-6xcq: Erythromycin esterase EreC, mutant H289N in its closed conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xcq | ||||||
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Title | Erythromycin esterase EreC, mutant H289N in its closed conformation | ||||||
Components | EreC | ||||||
Keywords | HYDROLASE / Macrolide / esterase | ||||||
Function / homology | Erythromycin esterase, proteobacteria / Erythromycin esterase / Erythromycin esterase / response to antibiotic / S-1,2-PROPANEDIOL / EreC Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zielinski, M. / Park, J. / Berghuis, A.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural and functional insights into esterase-mediated macrolide resistance. Authors: Zielinski, M. / Park, J. / Sleno, B. / Berghuis, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xcq.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xcq.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xcq_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 6xcq_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 6xcq_validation.xml.gz | 19 KB | Display | |
Data in CIF | 6xcq_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/6xcq ftp://data.pdbj.org/pub/pdb/validation_reports/xc/6xcq | HTTPS FTP |
-Related structure data
Related structure data | 6xcsC 3b55S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48308.895 Da / Num. of mol.: 1 / Mutation: H289N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ereC / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: C7C425 |
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#2: Chemical | ChemComp-PGO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M phosphate-citrate pH 4.2, 5% (w/v) PEG 3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.152 Å / Num. obs: 27238 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.03177 / Net I/σ(I): 35.24 |
Reflection shell | Resolution: 2→2.072 Å / Mean I/σ(I) obs: 8.61 / Num. unique obs: 2699 / CC1/2: 0.981 / CC star: 0.995 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B55 Resolution: 2→28.15 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.15 Å
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Refine LS restraints |
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LS refinement shell |
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