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- PDB-6gos: E. coli Microcin synthetase McbBCD complex with pro-MccB17 bound -

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Basic information

Entry
Database: PDB / ID: 6gos
TitleE. coli Microcin synthetase McbBCD complex with pro-MccB17 bound
Components
  • (Microcin B17-processing protein ...) x 3
  • Bacteriocin microcin B17
KeywordsAntibiotic/inhibitor / microcin / DNA gyrase / heterocyclization / posttranslational modification / BIOSYNTHETIC PROTEIN / Antibiotic-inhibitor complex
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 / SAD / Resolution: 2.1 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 4, 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)151,89018
Polymers150,6715
Non-polymers1,21913
Water6,936385
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)303,78036
Polymers301,34210
Non-polymers2,43726
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area56300 Å2
ΔGint-284 kcal/mol
Surface area84370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.960, 83.400, 86.900
Angle α, β, γ (deg.)90.00, 91.45, 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: 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.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: mcbA / Plasmid: pBAD-HisMcbABCDEFG / 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-HisMcbABCDEFG / 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
Source method: isolated from a genetically manipulated source
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 , 7 types, 398 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


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


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.63 %
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: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1510.21.48954950.540.4851.56898.4
9.39-57.399.70.0488950.9980.0160.0599.5

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→57.39 Å / SU B: 12.354 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3821 5.1 %RANDOM
Rwork0.172 ---
obs0.174 71582 99.8 %-
Displacement parametersBiso mean: 43.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.12 Å2
2--1.14 Å20 Å2
3----1.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→57.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9830 0 131 385 10346

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