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- PDB-8c6y: PBP AccA from A. tumefaciens Bo542 in apoform 2 -

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Basic information

Entry
Database: PDB / ID: 8c6y
TitlePBP AccA from A. tumefaciens Bo542 in apoform 2
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homologyPeptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / Agrocinopine utilization periplasmic binding protein AccA
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsMorera, S. / Vigouroux, A. / legrand, P.
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
DepositionJan 12, 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)56,3562
Polymers56,2941
Non-polymers621
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.878, 58.889, 177.793
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


Mass: 56293.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: Bo542 / Gene: accA, AgrTiChry5_232
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2P0QK24
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, Na citrate, AcNH4

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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: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 40544 / % possible obs: 66.9 % / Redundancy: 14 % / CC1/2: 0.998 / Rmerge(I) obs: 0.188 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 1.832 / Num. unique obs: 2912 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→22.68 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.322 / SU Rfree Blow DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1328 -RANDOM
Rwork0.2181 ---
obs0.2201 27409 67.7 %-
Displacement parametersBiso mean: 26.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.7527 Å20 Å20 Å2
2--0.2134 Å20 Å2
3---2.5393 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.901→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 4 296 4203
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097866HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0414220HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2302SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1227HARMONIC5
X-RAY DIFFRACTIONt_it7861HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion514SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6752SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion15.33
LS refinement shellResolution: 1.901→1.96 Å
RfactorNum. reflection% reflection
Rfree0.2517 29 -
Rwork0.28 --
obs--15.9 %

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