+Open data
-Basic information
Entry | Database: PDB / ID: 6gri | |||||||||||||||
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Title | E. coli Microcin synthetase McbBCD complex | |||||||||||||||
Components | (Microcin B17-processing protein ...) x 3 | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / microcin / DNA gyrase / heterocyclization / posttranslational modification | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 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 | 6gri.cif.gz | 482 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gri.ent.gz | 390.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/6gri ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6gri | HTTPS FTP |
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-Related structure data
Related structure data | 6gosSC 6grgC 6grhC 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
-Microcin B17-processing protein ... , 3 types, 4 molecules 12CD
#1: Protein | Mass: 34032.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcbB / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23184 #2: Protein | | Mass: 30789.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcbC / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23185 #3: Protein | | Mass: 44963.973 Da / Num. of mol.: 1 Mutation: There is a T171R substitution relative to UniProtKB sequence Source method: isolated from a genetically manipulated source Details: There is a T171R substitution relative to UniProtKB sequence. Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcbD / Plasmid: pBAD-McbABCDEFG / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23186 |
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-Non-polymers , 5 types, 45 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FMN / | #8: 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: 2.3 Å3/Da / Density % sol: 46.45 % |
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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: I03 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 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: 2.7→91.92 Å / Num. obs: 35976 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Net I/σ(I): 13.1 / Num. measured all: 245530 | ||||||||||||||||||||||||
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: 2.7→91.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 38.236 / SU ML: 0.349 / SU R Cruickshank DPI: 0.2986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.52 Å2 / Biso mean: 71.067 Å2 / Biso min: 34.49 Å2
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Refinement step | Cycle: final / Resolution: 2.7→91.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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