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- PDB-5ofr: Structure of the antibacterial peptide ABC transporter McjD in a ... -

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Basic information

Entry
Database: PDB / ID: 5ofr
TitleStructure of the antibacterial peptide ABC transporter McjD in a high energy outward occluded intermediate state
ComponentsMicrocin-J25 export ATP-binding/permease protein McjD
KeywordsMEMBRANE PROTEIN / ABC transporter / antibacterial peptide / high energy outward occluded intermediate / ADP-VO4
Function / homology
Function and homology information


bacteriocin transport / bacteriocin immunity / ABC-type oligopeptide transporter activity / protein transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Microcin-J25 export ATP-binding/permease protein McjD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBeis, K. / Bountra, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N020103/1 United Kingdom
Citation
Journal: EMBO J. / Year: 2017
Title: Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD.
Authors: Bountra, K. / Hagelueken, G. / Choudhury, H.G. / Corradi, V. / El Omari, K. / Wagner, A. / Mathavan, I. / Zirah, S. / Yuan Wahlgren, W. / Tieleman, D.P. / Schiemann, O. / Rebuffat, S. / Beis, K.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.
Authors: Choudhury, H.G. / Tong, Z. / Mathavan, I. / Li, Y. / Iwata, S. / Zirah, S. / Rebuffat, S. / van Veen, H.W. / Beis, K.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / software / struct_conn
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 / _software.name / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microcin-J25 export ATP-binding/permease protein McjD
B: Microcin-J25 export ATP-binding/permease protein McjD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0988
Polymers130,9652
Non-polymers1,1336
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-137 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.290, 105.040, 117.370
Angle α, β, γ (deg.)90.00, 105.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Microcin-J25 export ATP-binding/permease protein McjD / Microcin-J25 immunity protein / Microcin-J25 secretion ATP-binding protein McjD


Mass: 65482.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcjD
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: UniProt: Q9X2W0
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION

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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: 5.33 Å3/Da / Density % sol: 76.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol

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Data collection

DiffractionMean temperature: 60 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.26 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.26 Å / Relative weight: 1
ReflectionResolution: 3.4→95.3 Å / Num. obs: 22352 / % possible obs: 94.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 98.36 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.1
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 437 / CC1/2: 0.86 / % possible all: 87.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pl0

4pl0


Resolution: 3.4→95.3 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.835 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.647
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1068 4.78 %RANDOM
Rwork0.257 ---
obs0.257 22350 58.6 %-
Displacement parametersBiso mean: 108.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.9021 Å20 Å2-14.0367 Å2
2--3.6782 Å20 Å2
3----4.5803 Å2
Refine analyzeLuzzati coordinate error obs: 0.63 Å
Refinement stepCycle: 1 / Resolution: 3.4→95.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 66 0 9161
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019328HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1112647HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4404SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes216HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1356HARMONIC5
X-RAY DIFFRACTIONt_it9328HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion3.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1279SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11188SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.231 -4.75 %
Rwork0.248 1204 -
all0.247 1264 -
obs--25.18 %

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