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- PDB-8ch1: PBP AccA from A. vitis S4 in complex with Agrocinopine A -

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Basic information

Entry
Database: PDB / ID: 8ch1
TitlePBP AccA from A. vitis S4 in complex with Agrocinopine A
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology: / : / 2-O-phosphono-alpha-L-arabinopyranose / DI(HYDROXYETHYL)ETHER / 2-O-phosphono-beta-L-arabinopyranose
Function and homology information
Biological speciesAgrobacterium vitis S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 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 6, 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

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Assembly

Deposited unit
A: Agrocinopine utilization periplasmic binding protein AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0909
Polymers56,6521
Non-polymers1,4378
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint16 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.1, 60.61, 151.28
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Agrocinopine utilization periplasmic binding protein AccA


Mass: 56652.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis S4 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: phosphodiester of sucrose and L-arabinose / References: BIRD: PRD_002473
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
#3: Sugar ChemComp-VDF / 2-O-phosphono-beta-L-arabinopyranose / 2-O-phosphono-beta-L-arabinose / 2-O-phosphono-L-arabinose / 2-O-phosphono-arabinose / [(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate


Type: L-saccharide, beta linking, Oligosaccharide / Class: Nutrient / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Details: phosphodiester of sucrose and L-arabinose / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002473
#4: Sugar ChemComp-LAO / 2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-alpha-L-arabinose / 2-O-phosphono-L-arabinose / 2-O-phosphono-arabinose


Type: L-saccharide, alpha linking, Oligosaccharide / Class: Nutrient / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Details: phosphodiester of sucrose and L-arabinose / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002470

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Non-polymers , 3 types, 455 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsA member of the class of agrocinopines that consists of sucrose and L-arabinose units joined via a ...A member of the class of agrocinopines that consists of sucrose and L-arabinose units joined via a phosphodiester linkage between position 4F of sucrose and position 2 of arabinose.
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: 35.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.496→47.3 Å / Num. obs: 70531 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9
Reflection shellResolution: 1.496→1.59 Å / Rmerge(I) obs: 1.303 / Num. unique obs: 10968 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.496→47.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 3527 -RANDOM
Rwork0.1741 ---
obs0.1755 70531 99.5 %-
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.5583 Å20 Å20 Å2
2--4.1401 Å20 Å2
3----1.5819 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.496→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 56 451 4316
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017822HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114135HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2287SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1191HARMONIC5
X-RAY DIFFRACTIONt_it7822HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion518SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7721SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.9
X-RAY DIFFRACTIONt_other_torsion14.56
LS refinement shellResolution: 1.496→1.51 Å
RfactorNum. reflection% reflection
Rfree0.3854 71 -
Rwork0.3514 --
obs0.3532 1411 80.93 %
Refinement TLS params.Origin x: 17.6356 Å / Origin y: -1.327 Å / Origin z: -19.1469 Å
111213212223313233
T-0.0433 Å20.0246 Å20.0013 Å2--0.03 Å2-0.0129 Å2---0.0921 Å2
L0.3732 °20.0523 °20.0612 °2-0.9952 °2-0.1153 °2--0.3466 °2
S-0.0203 Å °0.2951 Å °-0.0415 Å °0.2951 Å °0.0272 Å °-0.0072 Å °-0.0415 Å °-0.0072 Å °-0.0068 Å °
Refinement TLS groupSelection details: { A|* }

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