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Yorodumi- PDB-6grg: E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6grg | |||||||||||||||
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Title | E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate bound | |||||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / microcin / DNA gyrase / heterocyclization / posttranslational modification | |||||||||||||||
Function / homology | Function and homology information negative regulation of DNA replication / antibiotic biosynthetic process / killing of cells of another organism / oxidoreductase activity / defense response to bacterium / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å | |||||||||||||||
Authors | Ghilarov, D. / Stevenson, C.E.M. / Travin, D.Y. / Piskunova, J. / Serebryakova, M. / Maxwell, A. / Lawson, D.M. / Severinov, K. | |||||||||||||||
Funding support | Poland, Russian Federation, United Kingdom, 4items
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Citation | Journal: Mol. Cell / Year: 2019 Title: Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Authors: Ghilarov, D. / Stevenson, C.E.M. / Travin, D.Y. / Piskunova, J. / Serebryakova, M. / Maxwell, A. / Lawson, D.M. / Severinov, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6grg.cif.gz | 521 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6grg.ent.gz | 420.6 KB | Display | PDB format |
PDBx/mmJSON format | 6grg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/6grg ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6grg | HTTPS FTP |
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-Related structure data
Related structure data | 6gosSC 6grhC 6griC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 6853.401 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The McbA protein was expressed with an eight-residue nickel affinity tag with sequence MGHHHHHH appended to the N-terminus of the full-length amino acid sequence. It was subsequently post- ...Details: The McbA protein was expressed with an eight-residue nickel affinity tag with sequence MGHHHHHH appended to the N-terminus of the full-length amino acid sequence. It was subsequently post-translationally modified by the McbBCD complex to yield nine heterocycles, where F6N equals oxazole and is derived from Gly-Ser, F75 equals thiazole and is derived from Gly-Cys, OTZ equals oxazole-thiazole and is derived from Gly-Ser-Cys, TOZ equals thiazole-oxazole and is derived from Gly-Cys-Ser. Each mono- or bis-heterocycle (where present) was treated as a pseudo-amino acid for refinement purposes. The numbering system used in this PDB file relates to the processed peptide where each pseudo-amino acid is treated as a single residue making the overall sequence nine residues shorter. Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: mcbA / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P05834 |
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-Microcin B17-processing protein ... , 3 types, 4 molecules 12CD
#2: Protein | Mass: 34032.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: mcbB / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23184 #3: Protein | | Mass: 30789.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: mcbC / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23185 #4: Protein | | Mass: 44963.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: There is a T171R substitution relative to UniProtKB sequence Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: mcbD / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23186 |
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-Non-polymers , 11 types, 240 molecules
#5: Chemical | ChemComp-FMN / | ||||||||||||||||||
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#6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-GOL / | #9: Chemical | ChemComp-ATP / | #10: Chemical | #11: Chemical | ChemComp-ADP / | #12: Chemical | ChemComp-PO4 / | #13: Chemical | #14: Chemical | ChemComp-CL / | #15: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.35→86.76 Å / Num. obs: 53732 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.054 / Rrim(I) all: 0.15 / Net I/σ(I): 11.6 / Num. measured all: 409359 / Scaling rejects: 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6GOS Resolution: 2.35→86.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.941 / SU B: 20.463 / SU ML: 0.225 / SU R Cruickshank DPI: 0.4202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.243 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.28 Å2 / Biso mean: 53.476 Å2 / Biso min: 27.57 Å2
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Refinement step | Cycle: final / Resolution: 2.35→86.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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