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- PDB-3h9g: Crystal structure of E. coli MccB + MccA-N7isoASN -

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Basic information

Entry
Database: PDB / ID: 3h9g
TitleCrystal structure of E. coli MccB + MccA-N7isoASN
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 / 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
Microcin C7 iso-ASN analog / Microcin C7 / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10, 2013Group: Other
Revision 1.5Nov 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 1.6Sep 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)161,62919
Polymers160,6948
Non-polymers93411
Water9,206511
1
A: MccB protein
B: MccB protein
E: Microcin C7 analog
F: Microcin C7 analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7669
Polymers80,3474
Non-polymers4195
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-58 kcal/mol
Surface area25090 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)80,86210
Polymers80,3474
Non-polymers5156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-50.4 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.929, 138.217, 80.799
Angle α, β, γ (deg.)90.00, 92.38, 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


Type: PolypeptidePeptide / Class: Inhibitor / Mass: 763.844 Da / Num. of mol.: 4 / Mutation: ASN 7 to XSN, Iso asparagine / Source method: obtained synthetically
Details: MRTGNA-N7isoAsn was synthesized as previously described (Novoa et al, 1986; Roush et. al. 2008)
Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q47505, Microcin C7 iso-ASN analog
#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.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Tris-HCl pH 8.0, 50 mM (NH4)2SO4, 10 mM MccA-N7isoAsn, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2007 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock high-resolution double crystal Si(220) sagital focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 60798 / Num. obs: 60798 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.152 / Net I/σ(I): 21.914
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.371 / Num. unique all: 5645 / Χ2: 0.822 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
X-GENdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H5A

3h5a


Resolution: 2.2→46.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU B: 7.969 / SU ML: 0.202 / SU R Cruickshank DPI: 0.451 / SU Rfree: 0.263 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.451 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3041 5.1 %RANDOM
Rwork0.203 ---
all0.206 62124 --
obs0.203 60091 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 36.297 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.03 Å2
2---1.05 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10767 0 39 511 11317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211012
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.94914959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2851381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.14224.848495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.297151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6411547
X-RAY DIFFRACTIONr_chiral_restr0.0750.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028371
X-RAY DIFFRACTIONr_nbd_refined0.2010.25398
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2765
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.218
X-RAY DIFFRACTIONr_mcbond_it0.7941.57107
X-RAY DIFFRACTIONr_mcangle_it1.116211129
X-RAY DIFFRACTIONr_scbond_it1.59134472
X-RAY DIFFRACTIONr_scangle_it2.2174.53830
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 189 -
Rwork0.26 3940 -
all-4129 -
obs--89.84 %

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