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- PDB-3h5r: Crystal structure of E. coli MccB + Succinimide -

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Basic information

Entry
Database: PDB / ID: 3h5r
TitleCrystal structure of E. coli MccB + Succinimide
Components
  • MccB protein
  • Microcin C7 analog
KeywordsTRANSFERASE/ANTIBIOTIC / Ubiquitin-activating enzyme / microcin / bacteriocin / Mcc7 / peptide antibiotic / N-P bond formation / Antibiotic / Antimicrobial / Phosphoprotein / TRANSFERASE / TRANSFERASE-ANTIBIOTIC COMPLEX
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 / Outer Surface Protein A; domain 3 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Microcin C7 / Microcin C7 / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRegni, C.A. / Roush, R.F. / Miller, D. / Nourse, A. / Walsh, C.T. / Schulman, B.A.
CitationJournal: Embo J. / Year: 2009
Title: How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.
Authors: Regni, C.A. / Roush, R.F. / Miller, D.J. / Nourse, A. / Walsh, C.T. / Schulman, B.A.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Non-polymer description / Structure summary
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_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: MccB protein
D: MccB protein
E: Microcin C7 analog
F: Microcin C7 analog
G: Microcin C7 analog
H: Microcin C7 analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,07614
Polymers160,6228
Non-polymers4546
Water4,738263
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19290 Å2
ΔGint-98.8 kcal/mol
Surface area51650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.934, 137.972, 80.134
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MccB protein /


Mass: 39409.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: thrombin cleavable His-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BM7006 / Gene: mccB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47506
#2: Protein/peptide
Microcin C7 analog / MccC7 / Microcin C51 / MccC51 / Microcin C / McC


Type: PolypeptidePeptide / Class: Inhibitor / Mass: 745.829 Da / Num. of mol.: 4 / Mutation: ASN 7 to SNN, cyclized asparagine / Source method: obtained synthetically
Details: MRTGNA-succinimide was synthesized as previously described (Novoa et al, 1986; Roush et al, 2008).
Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q47505, Microcin C7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24-26% pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Bis-Tris pH 6.5, 50 mM (NH4)2SO4, 10 mM Succinimidyl peptide, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2008
Details: Sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(111) sagital focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 71440 / Num. obs: 71440 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.181
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.546 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
X-GENdata scaling
HKL-2000data reduction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H5N

3h5n


Resolution: 2.1→27.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.766 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24995 3553 5 %RANDOM
Rwork0.19375 ---
obs0.19658 70567 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.108 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0.35 Å2
2---1.33 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10435 0 14 263 10712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210655
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.94714478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40551350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75724.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.778151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0051543
X-RAY DIFFRACTIONr_chiral_restr0.110.21641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028089
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.25015
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.27341
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2500
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921.56937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.378210839
X-RAY DIFFRACTIONr_scbond_it2.24734277
X-RAY DIFFRACTIONr_scangle_it3.2524.53639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 234 -
Rwork0.238 4998 -
obs--99.89 %

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