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- PDB-5ofp: Structure of the antibacterial peptide ABC transporter McjD in an... -

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Basic information

Entry
Database: PDB / ID: 5ofp
TitleStructure of the antibacterial peptide ABC transporter McjD in an apo inward occluded conformation
ComponentsMicrocin-J25 export ATP-binding/permease protein McjD
KeywordsMEMBRANE PROTEIN / ABC transporter / antibacterial peptide / apo / inward occluded
Function / homology
Function and homology information


bacteriocin transport / bacteriocin immunity / ATPase-coupled lipid transmembrane transporter activity / ABC-type 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Microcin-J25 export ATP-binding/permease protein McjD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.71 Å
AuthorsBeis, K. / Choudhury, H.G.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)65,4821
Polymers65,4821
Non-polymers00
Water00
1
A: Microcin-J25 export ATP-binding/permease protein McjD

A: Microcin-J25 export ATP-binding/permease protein McjD


Theoretical massNumber of molelcules
Total (without water)130,9652
Polymers130,9652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11380 Å2
ΔGint-89 kcal/mol
Surface area50330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.850, 87.850, 351.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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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.: 1
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

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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: 5.18 Å3/Da / Density % sol: 76.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 5 mM MgCl2, 24 % PEG400 and 100 mM glycine pH 9.0

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Data collection

DiffractionMean temperature: 60 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.71→78.58 Å / Num. obs: 7675 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 260.22 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.6
Reflection shellResolution: 4.71→4.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2025 / CC1/2: 0.65 / % possible all: 94.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pl0

4pl0


Resolution: 4.71→30.06 Å / Cor.coef. Fo:Fc: 0.6458 / Cor.coef. Fo:Fc free: 0.72 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.232
RfactorNum. reflection% reflectionSelection details
Rfree0.3344 376 4.93 %RANDOM
Rwork0.3133 ---
obs0.3143 7623 98.27 %-
Displacement parametersBiso mean: 96.53 Å2
Baniso -1Baniso -2Baniso -3
1--44.5046 Å20 Å20 Å2
2---44.5046 Å20 Å2
3---89.0092 Å2
Refine analyzeLuzzati coordinate error obs: 1.24 Å
Refinement stepCycle: 1 / Resolution: 4.71→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4527 0 0 0 4527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014603HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046234HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2174SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4603HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.12
X-RAY DIFFRACTIONt_other_torsion3.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion632SEMIHARMONIC5
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_contact5442SEMIHARMONIC4
LS refinement shellResolution: 4.71→5.26 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3875 116 5.64 %
Rwork0.2801 1942 -
all0.2866 2058 -
obs--98.27 %

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