6GOS

E. coli Microcin synthetase McbBCD complex with pro-MccB17 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison.

Ghilarov, D.Stevenson, C.E.M.Travin, D.Y.Piskunova, J.Serebryakova, M.Maxwell, A.Lawson, D.M.Severinov, K.

(2019) Mol. Cell 73: 749-762.e5


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriocin microcin B17
A
77Escherichia coliMutation(s): 0 
Gene Names: mcbA
Find proteins for P05834 (Escherichia coli)
Go to UniProtKB:  P05834
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Microcin B17-processing protein McbB
1, 2
295Escherichia coliMutation(s): 0 
Gene Names: mcbB
Find proteins for P23184 (Escherichia coli)
Go to UniProtKB:  P23184
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Microcin B17-processing protein McbC
C
272Escherichia coliMutation(s): 0 
Gene Names: mcbC
Find proteins for P23185 (Escherichia coli)
Go to UniProtKB:  P23185
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Microcin B17-processing protein McbD
D
396Escherichia coliMutation(s): 0 
Gene Names: mcbD
Find proteins for P23186 (Escherichia coli)
Go to UniProtKB:  P23186
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
1, 2
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
1
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
C
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
1, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
2, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
F6N
Query on F6N
A
peptide linkingC5 H6 N2 O3GLY, SER
F75
Query on F75
A
peptide linkingC5 H6 N2 O2 SGLY, CYS
OTZ
Query on OTZ
A
peptide linkingC8 H7 N3 O3 SGLY, SER, CYS
TOZ
Query on TOZ
A
peptide linkingC8 H7 N3 O3 SGLY, CYS, SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 180.960α = 90.00
b = 83.400β = 91.45
c = 86.900γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CRANK2phasing
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionPolandMarie Sklodowska-Curie grant agreement No 665778
Russian Foundation for Basic ResearchRussian FederationRFBR-Royal Society International Exchanges Scheme (KO165410043/IE160246)
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012523/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references