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- PDB-5eg1: Antibacterial peptide ABC transporter McjD with a resolved lipid -

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Basic information

Entry
Database: PDB / ID: 5eg1
TitleAntibacterial peptide ABC transporter McjD with a resolved lipid
ComponentsMicrocin-J25 export ATP-binding/permease protein McjD
KeywordsTRANSPORT PROTEIN / membrane protein / ABC transporter / lipid
Function / homology
Function and homology information


bacteriocin transport / bacteriocin immunity / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-P6L / Microcin-J25 export ATP-binding/permease protein McjD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsChoudhury, H.G. / Beis, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H01778X/1 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD.
Authors: Mehmood, S. / Corradi, V. / Choudhury, H.G. / Hussain, R. / Becker, P. / Axford, D. / Zirah, S. / Rebuffat, S. / Tieleman, D.P. / Robinson, C.V. / 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
DepositionOct 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)132,7737
Polymers130,9652
Non-polymers1,8085
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17080 Å2
ΔGint-124 kcal/mol
Surface area47460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.980, 109.130, 233.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Plasmid: PWALDOGFPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9X2W0
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate pH 5.5, 45 mM NaCl, 28% PEG 400 and 1% nonyl-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.42→67.61 Å / Num. obs: 29066 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.87 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 3.42→3.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PL0

4pl0


Resolution: 3.42→67.61 Å / Cor.coef. Fo:Fc: 0.7807 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.513
Details: Due to low resolution of the data, the ligand head group could either a glycerol or ethanolamine moiety. We assigned it as glycerol since it was supported by our biochemical data. Both head ...Details: Due to low resolution of the data, the ligand head group could either a glycerol or ethanolamine moiety. We assigned it as glycerol since it was supported by our biochemical data. Both head groups can be refined without the presence of any negative Fo-Fc density
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 1458 5.02 %RANDOM
Rwork0.2535 ---
obs0.2544 29028 98.7 %-
Displacement parametersBiso mean: 126.14 Å2
Baniso -1Baniso -2Baniso -3
1--62.3634 Å20 Å20 Å2
2---17.7063 Å20 Å2
3---80.0697 Å2
Refine analyzeLuzzati coordinate error obs: 1.298 Å
Refinement stepCycle: 1 / Resolution: 3.42→67.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9107 0 115 0 9222
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019378HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0712705HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4452SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes216HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1360HARMONIC5
X-RAY DIFFRACTIONt_it9378HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion3.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1281SEMIHARMONIC5
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_contact11154SEMIHARMONIC4
LS refinement shellResolution: 3.42→3.54 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3042 145 5.19 %
Rwork0.2998 2649 -
all0.3 2794 -
obs--98.7 %

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