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- PDB-8ch3: PBP AccA from A. vitis S4 in complex with Agrocinopine C-like -

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Basic information

Entry
Database: PDB / ID: 8ch3
TitlePBP AccA from A. vitis S4 in complex with Agrocinopine C-like
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology: / 2-O-phosphono-alpha-D-glucopyranose
Function and homology information
Biological speciesAgrobacterium vitis S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 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)57,2553
Polymers56,6521
Non-polymers6022
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint10 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.83, 60.71, 151.39
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.) Agrobacterium vitis S4 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphodiester of D-alpha-glucose (ALX) and sucrose (GLC-FRU).
References: BIRD: PRD_002506
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
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-ALX / 2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-alpha-D-glucose / 2-O-phosphono-D-glucose / 2-O-phosphono-glucose


Type: D-saccharide, alpha linking, Oligosaccharide / Class: Nutrient / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
Details: Phosphodiester of D-alpha-glucose (ALX) and sucrose (GLC-FRU).
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002506
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIsomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of ...Isomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of sucrose and D-glucose joined via a phosphodiester linkage.
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: 1.9 Å3/Da / Density % sol: 35.24 %
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 2 / Wavelength: 0.980101 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980101 Å / Relative weight: 1
ReflectionResolution: 1.398→47.36 Å / Num. obs: 85091 / % possible obs: 98.9 % / Redundancy: 11 % / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.19
Reflection shellResolution: 1.398→1.48 Å / Rmerge(I) obs: 2.364 / Num. unique obs: 13395 / CC1/2: 0.459

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.398→20.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 4255 -RANDOM
Rwork0.1897 ---
obs0.1911 85091 98.6 %-
Displacement parametersBiso mean: 33.11 Å2
Baniso -1Baniso -2Baniso -3
1--3.9512 Å20 Å20 Å2
2--4.1946 Å20 Å2
3----0.2434 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.398→20.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 38 403 4255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117824HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1314151HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2293SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1204HARMONIC5
X-RAY DIFFRACTIONt_it7824HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion524SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7721SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5
X-RAY DIFFRACTIONt_other_torsion14.23
LS refinement shellResolution: 1.398→1.41 Å
RfactorNum. reflection% reflection
Rfree0.415 85 -
Rwork0.3665 --
obs0.3689 1702 89.72 %
Refinement TLS params.Origin x: 17.641 Å / Origin y: -1.3259 Å / Origin z: -19.1493 Å
111213212223313233
T-0.0509 Å20.0153 Å2-0.0053 Å2--0.1248 Å2-0.0167 Å2---0.1598 Å2
L0.4029 °20.0849 °2-0.0141 °2-1.2995 °2-0.1939 °2--0.4541 °2
S-0.0015 Å °0.4423 Å °-0.0633 Å °0.4423 Å °0.005 Å °-0.0013 Å °-0.0633 Å °-0.0013 Å °-0.0035 Å °
Refinement TLS groupSelection details: { A|* }

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