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- PDB-3h9j: Crystal structure of E. coli MccB + AMPCPP + SeMeT MccA -

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Basic information

Entry
Database: PDB / ID: 3h9j
TitleCrystal structure of E. coli MccB + AMPCPP + 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 sulfurtransferase activity / nucleotidyltransferase activity / defense response to bacterium / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Outer Surface Protein A; domain 3 - #70 / Outer Surface Protein A; domain 3 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / 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 / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Microcin C7 / MccB protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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: 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_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 1.8Oct 30, 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)163,76618
Polymers160,8828
Non-polymers2,88410
Water4,017223
1
A: MccB protein
B: MccB protein
E: Microcin C7 ANALOG
F: Microcin C7 ANALOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6789
Polymers80,4414
Non-polymers1,2375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-43.5 kcal/mol
Surface area26650 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)82,0879
Polymers80,4414
Non-polymers1,6465
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-46.2 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.841, 138.004, 80.816
Angle α, β, γ (deg.)90.000, 92.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#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: (MSE)RTGNAN 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

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Non-polymers , 4 types, 233 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 9 mM AMPCPP, 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: 2.3→50 Å / Num. all: 54611 / Num. obs: 54611 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.103 / Net I/σ(I): 17.14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.364 / Num. unique all: 5027 / Χ2: 0.671 / % possible all: 91.1

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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: FOURIER SYNTHESIS
Starting model: PDB entry 3H9G

3h9g


Resolution: 2.3→39.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.81 / SU B: 17.693 / SU ML: 0.215 / SU R Cruickshank DPI: 0.568 / SU Rfree: 0.278 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.55 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2715 5.1 %RANDOM
Rwork0.196 ---
all0.203 54215 --
obs0.199 53753 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.47 Å2 / Biso mean: 44.194 Å2 / Biso min: 19.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0.08 Å2
2---1.57 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10482 0 142 223 10847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210845
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.96114759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87351349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.60524.916476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.999151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4881542
X-RAY DIFFRACTIONr_chiral_restr0.0830.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028180
X-RAY DIFFRACTIONr_nbd_refined0.1980.24949
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2501
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it0.5111.56952
X-RAY DIFFRACTIONr_mcangle_it0.912210856
X-RAY DIFFRACTIONr_scbond_it1.22934500
X-RAY DIFFRACTIONr_scangle_it1.9724.53903
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 165 -
Rwork0.242 3488 -
all-3653 -
obs--91.95 %

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