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- PDB-8ckd: PBP AccA from A. fabrum C58 in complex with agrocinopine D-like -

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Basic information

Entry
Database: PDB / ID: 8ckd
TitlePBP AccA from A. fabrum C58 in complex with agrocinopine D-like
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
Chem-Y45 / Chem-Y4H / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)58,2096
Polymers57,1781
Non-polymers1,0315
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint6 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 108.220, 113.130
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-355-

ARG

21A-355-

ARG

31A-1035-

HOH

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Components

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


Mass: 57178.102 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.6→42.2 Å / Num. obs: 63379 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.98
Reflection shellResolution: 1.6→1.71 Å / Rmerge(I) obs: 1.36 / Num. unique obs: 10139 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.088
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 3169 5 %RANDOM
Rwork0.1779 ---
obs0.1793 63379 100 %-
Displacement parametersBiso mean: 26.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.8565 Å20 Å20 Å2
2--0.396 Å20 Å2
3----3.2524 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 39 546 4530
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018131HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0314705HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2395SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1249HARMONIC5
X-RAY DIFFRACTIONt_it8131HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.66
X-RAY DIFFRACTIONt_other_torsion15.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion530SEMIHARMONIC5
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_contact8095SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.61 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4378 -4.97 %
Rwork0.3676 1205 -
all0.371 1268 -
obs--98.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°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)
10.63270.7401-0.16860.45440.13750.45780.0232-0.0795-0.08780.0414-0.0563-0.0218-0.02280.15080.0331-0.0284-0.0067-0.0130.04680.0561-0.035331.177620.3197153.237
20.41170.1274-0.04850.03550.04990.6667-0.0450.0169-0.0880.0033-0.0445-0.01870.04730.01520.08950.0050.00710.0402-0.0185-0.00420.003315.32167.622137.629
30.23960.1728-0.04830.16920.0610.242-0.0365-0.0201-0.05-0.0079-0.0175-0.00830.01550.03390.054-0.01730.00640.0148-0.00270.02050.000721.682914.7162143.491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|240 }A32 - 240
2X-RAY DIFFRACTION2{ A|241 - A|521 }A241 - 521
3X-RAY DIFFRACTION3{ A|604 - A|606 A|701 - A|1246 }A604 - 606
4X-RAY DIFFRACTION3{ A|604 - A|606 A|701 - A|1246 }A701 - 1246

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