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- PDB-8chc: PBP AccA from A. vitis S4 in complex with Agrocinopine D-like -

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Basic information

Entry
Database: PDB / ID: 8chc
TitlePBP AccA from A. vitis S4 in complex with Agrocinopine D-like
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homologyChem-Y45
Function and homology information
Biological speciesAllorhizobium ampelinum S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.679 Å
AuthorsMorera, S. / Vigouroux, A. / Deicsics, G.
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 7, 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)57,0752
Polymers56,6521
Non-polymers4221
Water5,999333
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 area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47, 60.85, 151.55
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agrocinopine utilization periplasmic binding protein AccA / 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)
#2: Chemical ChemComp-Y45 / Agrocinopine D-like (C2-C2 linked; with two alpha-D-glucopyranoses) / Agrocinopine D-like / bis[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate / D-glucose-2-phosphate-2-glucose


Mass: 422.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
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: 35.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.679→33.39 Å / Num. obs: 49148 / % possible obs: 97.1 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.8
Reflection shellResolution: 1.679→1.78 Å / Rmerge(I) obs: 1.59 / Num. unique obs: 6588 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.679→33.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2448 -RANDOM
Rwork0.1956 ---
obs0.1973 48967 96.8 %-
Displacement parametersBiso mean: 39.87 Å2
Baniso -1Baniso -2Baniso -3
1--9.6639 Å20 Å20 Å2
2--7.0253 Å20 Å2
3---2.6386 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.679→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 27 333 4169
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0513983HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2262SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1189HARMONIC5
X-RAY DIFFRACTIONt_it7736HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion515SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6940SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion15.06
LS refinement shellResolution: 1.679→1.71 Å
RfactorNum. reflection% reflection
Rfree0.5948 49 -
Rwork0.4603 --
obs0.4674 980 37.75 %
Refinement TLS params.Origin x: 17.641 Å / Origin y: -1.3259 Å / Origin z: -19.1493 Å
111213212223313233
T-0.0469 Å20.0353 Å2-0.0005 Å2--0.1964 Å2-0.0218 Å2---0.2575 Å2
L0.527 °20.1056 °20.1036 °2-1.3314 °2-0.1293 °2--0.7156 °2
S-0.0201 Å °0.4895 Å °-0.0424 Å °0.4895 Å °0.0336 Å °-0.0284 Å °-0.0424 Å °-0.0284 Å °-0.0135 Å °
Refinement TLS groupSelection details: { A|* }

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