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Yorodumi- PDB-6om4: The structure of Microcin C7 biosynthetic enzyme MccB in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6om4 | ||||||
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Title | The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / Microcin C7 / phosphoramidate / Trojan Horse Antibiotic | ||||||
Function / homology | Function and homology information URM1 activating enzyme activity / protein urmylation / tRNA wobble position uridine thiolation / sulfotransferase activity / thiosulfate sulfurtransferase activity / nucleotidyltransferase activity / defense response to bacterium / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dong, S.-H. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2019 Title: Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by theN-formyl of the peptide precursor. Authors: Dong, S.H. / Kulikovsky, A. / Zukher, I. / Estrada, P. / Dubiley, S. / Severinov, K. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6om4.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6om4.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 6om4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/6om4 ftp://data.pdbj.org/pub/pdb/validation_reports/om/6om4 | HTTPS FTP |
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-Related structure data
Related structure data | 3h9gS S: Starting model for refinement |
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Similar structure data |
-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
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 38853.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccB / Production host: Escherichia coli (E. coli) / References: UniProt: Q47506 #2: Protein/peptide | Mass: 792.839 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q47505 |
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-Non-polymers , 5 types, 449 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: 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: 1.73 Å3/Da / Density % sol: 29.02 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop Details: 0.1 M Magnesium formate, 15% w/v Polyethylene glycol 3350, and 6% w/v 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→65.98 Å / Num. obs: 59837 / % possible obs: 96.1 % / Redundancy: 14 % / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.7→1.725 Å / Num. unique obs: 4320 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H9G Resolution: 1.7→65.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.339 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.757 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→65.98 Å
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Refine LS restraints |
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