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- PDB-8cke: PBP AccA from A.tumefaciens C58 in complex with agrocinopine A in... -

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Basic information

Entry
Database: PDB / ID: 8cke
TitlePBP AccA from A.tumefaciens C58 in complex with agrocinopine A in space group I222
ComponentsABC transporter substrate-binding protein
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
: / : / ACETATE ION / 2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-beta-L-arabinopyranose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.298 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 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3567
Polymers56,0901
Non-polymers1,2666
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint13 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.923, 108.033, 112.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

21A-1146-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein


Mass: 56089.895 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: accA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q52012

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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: obtained synthetically / 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: isolated from a genetically manipulated source
Formula: C5H11O8P / Details: phosphodiester of sucrose and L-arabinose / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002473
#6: 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: isolated from a genetically manipulated source
Formula: C5H11O8P / Details: phosphodiester of sucrose and L-arabinose / References: BIRD: PRD_002470

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Non-polymers , 3 types, 459 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, NH4 acetate, citrate Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.298→78 Å / Num. obs: 78672 / % possible obs: 67.1 % / Redundancy: 13.7 % / Biso Wilson estimate: 15.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.5
Reflection shellResolution: 1.298→1.447 Å / Rmerge(I) obs: 1.6 / Num. unique obs: 3936 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.298→18.9 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.066
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 4033 5.13 %RANDOM
Rwork0.1538 ---
obs0.1554 78623 67.2 %-
Displacement parametersBiso mean: 19.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.3029 Å20 Å20 Å2
2--0.1232 Å20 Å2
3----0.4262 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.298→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 45 457 4456
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0128093HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1914631HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2365SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1232HARMONIC5
X-RAY DIFFRACTIONt_it8093HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.66
X-RAY DIFFRACTIONt_other_torsion15.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion527SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8121SEMIHARMONIC4
LS refinement shellResolution: 1.3→1.4 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2733 -6.17 %
Rwork0.2342 1476 -
all0.2366 1573 -
obs--6.84 %
Refinement TLS params.Method: refined / Origin x: 22.1558 Å / Origin y: 13.2318 Å / Origin z: 144.585 Å
111213212223313233
T-0.1134 Å20.0078 Å20.0095 Å2--0.1144 Å20.0232 Å2---0.0974 Å2
L0.5177 °20.265 °2-0.1262 °2-0.2734 °20.0475 °2--0.449 °2
S-0.0111 Å °-0.0599 Å °-0.0878 Å °-0.0001 Å °-0.0532 Å °-0.059 Å °0.0257 Å °0.0357 Å °0.0644 Å °
Refinement TLS groupSelection details: { A|* }

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