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- PDB-8cju: PBP AccA from A. vitis S4 in complex with agrocin84 -

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Basic information

Entry
Database: PDB / ID: 8cju
TitlePBP AccA from A. vitis S4 in complex with agrocin84
ComponentsABC transporter substrate binding protein (Agrocinopine)
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
: / Chem-UKU / ABC transporter substrate binding protein (Agrocinopine)
Similarity search - Component
Biological speciesAllorhizobium ampelinum S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.349 Å
AuthorsMorera, S. / Vigouroux, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2024
Title: A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.
Authors: Morera, S. / Vigouroux, A. / Aumont-Nicaise, M. / Ahmar, M. / Meyer, T. / El Sahili, A. / Deicsics, G. / Gonzalez-Mula, A. / Li, S. / Dore, J. / Sirigu, S. / Legrand, P. / Penot, C. / Andre, ...Authors: Morera, S. / Vigouroux, A. / Aumont-Nicaise, M. / Ahmar, M. / Meyer, T. / El Sahili, A. / Deicsics, G. / Gonzalez-Mula, A. / Li, S. / Dore, J. / Sirigu, S. / Legrand, P. / Penot, C. / Andre, F. / Faure, D. / Soulere, L. / Queneau, Y. / Vial, L.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate binding protein (Agrocinopine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3412
Polymers56,6521
Non-polymers6881
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.01, 60.74, 151.89
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter substrate binding protein (Agrocinopine)


Mass: 56652.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allorhizobium ampelinum S4 (bacteria) / Gene: accA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B9JXG4
#2: Chemical ChemComp-UKU / [(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid / Agrocin 84 (alpha-D-glucopyranose form)


Type: Oligosaccharide / Class: Nutrient / Mass: 688.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N6O16P2
Details: unusual glycan purine conjugate (containing GLC and ADE)
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002485
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Compound detailsConjugate contains alpha-D-glucose (GLC) and purine (ADE). The nucleoside core, which is essential ...Conjugate contains alpha-D-glucose (GLC) and purine (ADE). The nucleoside core, which is essential for toxicity, contains 3'-deoxyarabinose rather than ribose.
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.35→38.89 Å / Num. obs: 96419 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.86
Reflection shellResolution: 1.35→1.43 Å / Rmerge(I) obs: 1.065 / Num. unique obs: 15219 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.349→38.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 4821 -RANDOM
Rwork0.218 ---
obs0.2193 96419 99.8 %-
Displacement parametersBiso mean: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1--4.4164 Å20 Å20 Å2
2--4.4315 Å20 Å2
3----0.015 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.349→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 45 496 4350
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0127856HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.214219HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2296SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1211HARMONIC5
X-RAY DIFFRACTIONt_it7856HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion521SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7676SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.1
X-RAY DIFFRACTIONt_other_torsion11.72
LS refinement shellResolution: 1.35→1.36 Å
RfactorNum. reflection% reflection
Rfree0.3107 96 -
Rwork0.3347 --
obs0.3335 1929 92.65 %

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