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- PDB-6grg: E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP a... -

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Basic information

Entry
Database: PDB / ID: 6grg
TitleE. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / 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: 2.35 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)152,70819
Polymers150,6715
Non-polymers2,03714
Water4,071226
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)305,41738
Polymers301,34210
Non-polymers4,07428
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area55940 Å2
ΔGint-396 kcal/mol
Surface area86020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.640, 83.280, 86.790
Angle α, β, γ (deg.)90.000, 91.430, 90.000
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 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 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
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 / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#12: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#14: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.417.51.64139650.4220.6351.76399.5
10.51-86.766.90.036410.9990.0120.03299.3

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
Aimless0.5.17data scaling
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GOS

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2683 5 %RANDOM
Rwork0.1653 ---
obs0.1683 51049 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 144.28 Å2 / Biso mean: 53.476 Å2 / Biso min: 27.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.46 Å2
2--1.34 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.35→86.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9925 0 119 229 10273
Biso mean--61.93 47.25 -
Num. residues----1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01410340
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179234
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.66114010
X-RAY DIFFRACTIONr_angle_other_deg0.8871.6421581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.651251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66722.485511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.731151770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3351555
X-RAY DIFFRACTIONr_chiral_restr0.0670.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021978
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 199 -
Rwork0.305 3762 -
all-3961 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.325-3.45971.66025.4285-2.47131.2650.0594-0.01420.5214-0.2724-0.2778-0.4697-0.12390.01670.21840.54690.00270.09830.4593-0.24470.7352216.359727.803452.5504
23.0688-0.035-0.1240.9395-0.13380.8182-0.0351-0.31780.00560.08630.0211-0.01-0.09760.13210.0140.04220.00840.03520.1345-0.00270.0716194.985416.803865.002
30.5925-0.2581-0.50.8709-0.35793.1592-0.04990.096-0.192-0.12440.03030.02030.36370.09110.01970.06120.02680.04390.1618-0.00110.2493209.0417-2.71537.3309
40.8799-0.1991-0.08240.8081-0.00891.2786-0.01320.14040.254-0.0979-0.02640.0105-0.2741-0.02680.03950.0894-0.00430.01750.02390.02670.2197178.847945.407433.7537
51.0888-0.3048-0.31571.4449-0.12951.27540.00630.14260.0769-0.22520.023-0.1574-0.17310.347-0.02930.0886-0.10380.06280.2665-0.0050.1453215.608224.239814.3263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 59
2X-RAY DIFFRACTION2112 - 295
3X-RAY DIFFRACTION3213 - 294
4X-RAY DIFFRACTION4C2 - 266
5X-RAY DIFFRACTION5D1 - 396

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