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- PDB-8px9: Structure of the antibacterial peptide ABC transporter McjD, solv... -

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Basic information

Entry
Database: PDB / ID: 8px9
TitleStructure of the antibacterial peptide ABC transporter McjD, solved at wavelength 2.75 A
ComponentsMicrocin-J25 export ATP-binding/permease protein McjD
KeywordsMEMBRANE PROTEIN / ABC transporter
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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Microcin-J25 export ATP-binding/permease protein McjD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Bountra, K. / Beis, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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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)132,0266
Polymers130,9652
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-124 kcal/mol
Surface area46650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.190, 109.320, 233.350
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2W0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
Has ligand of interestN

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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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.8→54.67 Å / Num. obs: 51873 / % possible obs: 96.8 % / Redundancy: 54.6 % / Biso Wilson estimate: 83.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2146 / Rpim(I) all: 0.02965 / Rrim(I) all: 0.2167 / Net I/σ(I): 12.48
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 0.27 / Num. unique obs: 5092 / CC1/2: 0.675

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→54.67 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.873 / SU B: 103.209 / SU ML: 0.708 / Cross valid method: THROUGHOUT / ESU R: 0.693 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32974 2578 5 %RANDOM
Rwork0.29209 ---
obs0.29406 49306 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 163.335 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å20 Å20 Å2
2--3.23 Å20 Å2
3----7.91 Å2
Refinement stepCycle: 1 / Resolution: 2.8→54.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8913 0 64 0 8977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129218
X-RAY DIFFRACTIONr_bond_other_d0.0050.0168976
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.63612486
X-RAY DIFFRACTIONr_angle_other_deg0.7891.56120580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.39251130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.145544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.242101666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210524
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022142
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.5558.3274532
X-RAY DIFFRACTIONr_mcbond_other7.5558.3274532
X-RAY DIFFRACTIONr_mcangle_it11.39915.0765658
X-RAY DIFFRACTIONr_mcangle_other11.39915.0775659
X-RAY DIFFRACTIONr_scbond_it7.8449.0054686
X-RAY DIFFRACTIONr_scbond_other7.8439.0054686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.36116.3896829
X-RAY DIFFRACTIONr_long_range_B_refined18.144101.6337134
X-RAY DIFFRACTIONr_long_range_B_other18.144101.6337135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.58 186 -
Rwork0.578 3549 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4028-0.0004-0.2270.64540.65133.53850.04340.1205-0.15030.0316-0.0313-0.01330.7104-0.0268-0.0121.28130.0196-0.01541.0738-0.01150.072-22.2827-23.510642.431
20.31210.05410.27790.39030.1913.8277-0.01890.08940.0454-0.0842-0.05130.0942-0.4915-0.0810.07021.30950.0540.01931.0812-0.03190.0284-25.293-3.130740.1313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 601
2X-RAY DIFFRACTION2B8 - 601

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