+
Open data
-
Basic information
Entry | Database: PDB / ID: 6gos | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli Microcin synthetase McbBCD complex with pro-MccB17 bound | |||||||||||||||
![]() |
| |||||||||||||||
![]() | Antibiotic/inhibitor / microcin / DNA gyrase / heterocyclization / posttranslational modification / BIOSYNTHETIC PROTEIN / Antibiotic-inhibitor complex | |||||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Ghilarov, D. / Stevenson, C.E.M. / Travin, D.Y. / Piskunova, J. / Serebryakova, M. / Maxwell, A. / Lawson, D.M. / Severinov, K. | |||||||||||||||
Funding support | ![]() ![]() ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 510.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 430.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 834.8 KB | Display | |
Data in XML | ![]() | 47.2 KB | Display | |
Data in CIF | ![]() | 67.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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 the model 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.) ![]() ![]() Gene: mcbA / Plasmid: pBAD-HisMcbABCDEFG / Production host: ![]() ![]() |
---|
-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.) ![]() ![]() Gene: mcbB / Plasmid: pBAD-HisMcbABCDEFG / Production host: ![]() ![]() #3: Protein | | Mass: 30789.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mcbC / Plasmid: pBAD-McbABCDEFG / Production host: ![]() ![]() #4: Protein | | Mass: 44963.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mcbD / Plasmid: pBAD-McbABCDEFG / Production host: ![]() ![]() |
---|
-Non-polymers , 7 types, 398 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-FMN / | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→57.39 Å / Num. obs: 75405 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.049 / Rrim(I) all: 0.161 / Net I/σ(I): 10.7 / Num. measured all: 800263 / Scaling rejects: 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Displacement parameters | Biso mean: 43.82 Å2
| ||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→57.39 Å
|