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- PDB-8cay: PBP AccA from A. tumefaciens Bo542 in complex with Agrocinopine D-like -

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Basic information

Entry
Database: PDB / ID: 8cay
TitlePBP AccA from A. tumefaciens Bo542 in complex with Agrocinopine D-like
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology
Function and homology information


dipeptide transport / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-Y45 / Chem-Y4H / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.626 Å
AuthorsMorera, S. / Vigouroux, A. / Siragu, S.
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 24, 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: Agrocinopine utilization periplasmic binding protein AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3306
Polymers55,3341
Non-polymers9975
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-20 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.100, 40.209, 103.425
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Agrocinopine utilization periplasmic binding protein AccA / ABC transporter substrate binding protein (Agrocinopine)


Mass: 55333.684 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

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-Y4H / Agrocinopine D-like (C2-C2 linked; with an alpha and beta-D-glucopyranose) / Agrocinopine D-like / [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-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
#3: 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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, 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: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.626→53.2 Å / Num. obs: 50253 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.7 / Rmerge(I) obs: 0.238 / Net I/σ(I): 5.5
Reflection shellResolution: 1.626→1.78 Å / Rmerge(I) obs: 3.35 / Num. unique obs: 2610 / CC1/2: 0.11

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROC1.0.5 20200520data processing
autoPROCJan 31, 2020data processing
autoPROC2.3.36data processing
Aimless0.7.4data scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8C6R

8c6r


Resolution: 1.626→53.2 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.167 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.141
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1707 4.75 %RANDOM
Rwork0.1963 ---
obs0.1977 35908 70.6 %-
Displacement parametersBiso mean: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--4.5403 Å20 Å2-1.2184 Å2
2--8.2 Å20 Å2
3----3.6597 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.626→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 35 218 4157
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017938HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1114344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2339SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1233HARMONIC5
X-RAY DIFFRACTIONt_it7938HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.38
X-RAY DIFFRACTIONt_other_torsion15.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion525SEMIHARMONIC5
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_contact7461SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.71 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2758 -6.12 %
Rwork0.2431 675 -
all0.245 719 -
obs--10.32 %
Refinement TLS params.

L22: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2127-0.02260.4851-0.45450.7884-0.0966-0.1052-0.2265-0.00680.06690.0243-0.1220.03740.0296-0.07020.01640.00120.10720.0228-0.070612.4587-23.614736.3435
20.462-0.0105-0.0906-0.15110.50880.01140.0382-0.01820.0257-0.00990.0031-0.04570.0202-0.0015-0.0713-0.0135-0.01890.1196-0.018-0.063711.5552-12.930113.0286
30.3724-0.1395-0.1054-0.16790.4437-0.0203-0.0169-0.0382-0.00240.0050.006-0.0017-0.00090.0153-0.0816-0.0011-0.00940.1093-0.0085-0.04829.4987-17.636621.6752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|240 }A31 - 240
2X-RAY DIFFRACTION2{ A|241 - A|521 }A241 - 521
3X-RAY DIFFRACTION3{ A|701 - A|915 }A701 - 915

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