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- PDB-6om4: The structure of Microcin C7 biosynthetic enzyme MccB in complex ... -

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Basic information

Entry
Database: PDB / ID: 6om4
TitleThe structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA
Components
  • MccB protein
  • Microcin C7
KeywordsBIOSYNTHETIC PROTEIN / Microcin C7 / phosphoramidate / Trojan Horse Antibiotic
Function / homology
Function and homology information


ubiquitin-like modifier activating enzyme activity / defense response to bacterium / ATP binding / metal ion binding
Similarity search - Function
Outer Surface Protein A; domain 3 - #70 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Outer Surface Protein A; domain 3 / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine / PYROPHOSPHATE 2- / Microcin C7 / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, S.-H. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI117210 United States
CitationJournal: Chem Sci / Year: 2019
Title: Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by theN-formyl of the peptide precursor.
Authors: Dong, S.H. / Kulikovsky, A. / Zukher, I. / Estrada, P. / Dubiley, S. / Severinov, K. / Nair, S.K.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MccB protein
B: MccB protein
C: Microcin C7
D: Microcin C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,56414
Polymers79,2924
Non-polymers1,27210
Water7,909439
1
A: MccB protein
C: Microcin C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2827
Polymers39,6462
Non-polymers6365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-20 kcal/mol
Surface area17540 Å2
MethodPISA
2
B: MccB protein
D: Microcin C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2827
Polymers39,6462
Non-polymers6365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-21 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.094, 76.059, 131.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein MccB protein /


Mass: 38853.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccB / Production host: Escherichia coli (E. coli) / References: UniProt: Q47506
#2: Protein/peptide Microcin C7 / MccC7 / Microcin C51 / Microcin C


Mass: 792.839 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q47505

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Non-polymers , 5 types, 449 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-ND7 / 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine


Mass: 346.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N6O6P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 1.73 Å3/Da / Density % sol: 29.02 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Magnesium formate, 15% w/v Polyethylene glycol 3350, and 6% w/v 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.7→65.98 Å / Num. obs: 59837 / % possible obs: 96.1 % / Redundancy: 14 % / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.725 Å / Num. unique obs: 4320

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata scaling
PHENIXmodel building
BUCCANEERmodel building
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H9G

3h9g


Resolution: 1.7→65.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.339 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19868 2991 5 %RANDOM
Rwork0.1547 ---
obs0.15692 56811 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.757 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.57 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.7→65.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 24 439 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0145696
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175114
X-RAY DIFFRACTIONr_angle_refined_deg1.71.6857732
X-RAY DIFFRACTIONr_angle_other_deg1.071.66511958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47523.808281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1615936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5471523
X-RAY DIFFRACTIONr_chiral_restr0.0840.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021062
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7481.9072752
X-RAY DIFFRACTIONr_mcbond_other1.7471.9062751
X-RAY DIFFRACTIONr_mcangle_it2.5822.853433
X-RAY DIFFRACTIONr_mcangle_other2.5842.8513434
X-RAY DIFFRACTIONr_scbond_it2.8762.2442944
X-RAY DIFFRACTIONr_scbond_other2.8752.2442945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3393.2384300
X-RAY DIFFRACTIONr_long_range_B_refined5.21623.4646521
X-RAY DIFFRACTIONr_long_range_B_other5.21623.4626522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 215 -
Rwork0.219 4105 -
obs--94.2 %

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