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- PDB-3h9q: Crystal structure of E. coli MccB + SeMet MccA -

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Basic information

Entry
Database: PDB / ID: 3h9q
TitleCrystal structure of E. coli MccB + SeMet MccA
Components
  • MccB protein
  • Microcin C7 ANALOG
KeywordsTRANSFERASE/ANTIBIOTIC / Ubiquitin-activating enzyme / microcin / bacteriocin / Mcc7 / peptide antibiotic / N-P bond formation / Antibiotic / Antimicrobial / Formylation / Phosphoprotein / TRANSFERASE / TRANSFERASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


ubiquitin-like modifier activating enzyme activity / thiosulfate-cyanide sulfurtransferase activity / nucleotidyltransferase activity / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Outer Surface Protein A; domain 3 - #70 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / 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
Selenomethionine derivative of Microcin C7 / Microcin C7 / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.63 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 30, 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 1.4Jul 3, 2013Group: Other
Revision 1.5Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 1.6Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / 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 1.7Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Nov 6, 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: 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)161,33614
Polymers160,8828
Non-polymers4546
Water2,540141
1
A: MccB protein
B: MccB protein
E: Microcin C7 ANALOG
F: Microcin C7 ANALOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7648
Polymers80,4414
Non-polymers3234
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-46.9 kcal/mol
Surface area25940 Å2
MethodPISA
2
C: MccB protein
D: MccB protein
G: Microcin C7 ANALOG
H: Microcin C7 ANALOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5726
Polymers80,4414
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-53.1 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.300, 138.597, 81.375
Angle α, β, γ (deg.)90.000, 92.060, 90.000
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: Polypeptide / Class: Inhibitor / Mass: 810.739 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: MccA peptide was synthesized and reverse-phase HPLC purified by the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital
Source: (synth.) Escherichia coli (E. coli)
References: UniProt: Q47505, Selenomethionine derivative of 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


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


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.63 %
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 SeMet-MccA, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2007
Details: Vertical and horizontal focusing mirrors in Kirkpatrick-Baez geometry.
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce, optional Si(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.63→20 Å / Num. all: 37055 / Num. obs: 37055 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.082 / Net I/σ(I): 23.312
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.311 / Num. unique all: 3683 / Χ2: 0.546 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3H9J

3h9j


Resolution: 2.63→20 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1863 5 %RANDOM
Rwork0.207 ---
all0.207 36931 --
obs0.207 36931 99.9 %-
Solvent computationBsol: 27.884 Å2
Displacement parametersBiso max: 123.34 Å2 / Biso mean: 51.983 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-2.654 Å20 Å25.498 Å2
2---8.233 Å20 Å2
3---5.579 Å2
Refinement stepCycle: LAST / Resolution: 2.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10408 0 14 141 10563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.369
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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