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- PDB-6grh: E. coli Microcin synthetase McbBCD complex with truncated pro-Mcc... -

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Basic information

Entry
Database: PDB / ID: 6grh
TitleE. coli Microcin synthetase McbBCD complex with truncated pro-MccB17 bound
Components
  • (Microcin B17-processing protein ...) x 3
  • Bacteriocin microcin B17
KeywordsBIOSYNTHETIC 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
Microcin B17-processing protein McbB / SagB-type dehydrogenase domain / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Bacteriocin microcin B17 / Microcin B17-processing protein McbB / Microcin B17-processing protein McbC / Microcin B17-processing protein McbD
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsGhilarov, 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
OrganizationGrant numberCountry
European CommissionMarie Sklodowska-Curie grant agreement No 665778 Poland
Russian Foundation for Basic ResearchRFBR-Royal Society International Exchanges Scheme (KO165410043/IE160246) Russian Federation
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
CitationJournal: 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
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin microcin B17
1: Microcin B17-processing protein McbB
2: Microcin B17-processing protein McbB
C: Microcin B17-processing protein McbC
D: Microcin B17-processing protein McbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,24019
Polymers148,9595
Non-polymers1,28114
Water9,224512
1
A: Bacteriocin microcin B17
1: Microcin B17-processing protein McbB
2: Microcin B17-processing protein McbB
C: Microcin B17-processing protein McbC
D: Microcin B17-processing protein McbD
hetero molecules

A: Bacteriocin microcin B17
1: Microcin B17-processing protein McbB
2: Microcin B17-processing protein McbB
C: Microcin B17-processing protein McbC
D: Microcin B17-processing protein McbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,48038
Polymers297,91910
Non-polymers2,56128
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area53790 Å2
ΔGint-272 kcal/mol
Surface area85790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.740, 83.760, 87.120
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriocin microcin B17 / MccB17


Mass: 5141.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The mcbA gene is C-terminally truncated so that the unmodified peptide is only 46 residues long
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: mcbA / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P05834

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Microcin B17-processing protein ... , 3 types, 4 molecules 12CD

#2: Protein Microcin B17-processing protein McbB


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 Microcin B17-processing protein McbC


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 Microcin B17-processing protein McbD


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 str. K-12 substr. MG1655 (bacteria)
Gene: mcbD / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P23186

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Non-polymers , 7 types, 526 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→57.54 Å / Num. obs: 110695 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.435 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
Aimless0.5.26data scaling
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GOS

6gos


Resolution: 1.85→57.54 Å / SU B: 7.484 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5645 5.1 %RANDOM
Rwork0.172 ---
obs0.174 105049 99.8 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.3 Å2
2---0.02 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9861 0 89 512 10462

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