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- PDB-8caw: PBP AccA from A. tumefaciens Bo542 in complex with agrocin84 -

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Basic information

Entry
Database: PDB / ID: 8caw
TitlePBP AccA from A. tumefaciens Bo542 in complex with agrocin84
ComponentsAgrocinopine utilization periplasmic binding protein AccA
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
Similarity search - Domain/homology
: / : / Chem-C84 / Chem-UKU / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.256 Å
AuthorsMorera, S. / Vigouroux, A. / El Sahili, 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
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)56,7734
Polymers55,3341
Non-polymers1,4393
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint1 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.124, 51.093, 102.087
Angle α, β, γ (deg.)90.00, 109.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Agrocinopine utilization periplasmic binding protein AccA


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
#2: Chemical ChemComp-C84 / [(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid / Agrocin 84 (beta-D-glucopyranose form)


Type: Oligosaccharide / Class: Nutrient / Mass: 688.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N6O16P2
Details: unusual glycan purine conjugate (containing BGC and ADE)
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002484
#3: Chemical ChemComp-UKU / [(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid / Agrocin 84 (alpha-D-glucopyranose form)


Type: Oligosaccharide / Class: Nutrient / Mass: 688.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N6O16P2
Details: unusual glycan purine conjugate (containing GLC and ADE)
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002485
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Compound detailsConjugate contains beta-D-glucose (BGC) and purine (ADE). The nucleoside core, which is essential ...Conjugate contains beta-D-glucose (BGC) and purine (ADE). The nucleoside core, which is essential for toxicity, contains 3'-deoxyarabinose rather than ribose. Conjugate contains alpha-D-glucose (GLC) and purine (ADE). The nucleoside core, which is essential for toxicity, contains 3'-deoxyarabinose rather than ribose.
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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / 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 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.256→49.2 Å / Num. obs: 436693 / % possible obs: 91.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.5
Reflection shellResolution: 1.256→1.27 Å / Rmerge(I) obs: 1.91 / Num. unique obs: 3461 / CC1/2: 0.157

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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
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.256→18.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.061
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 4568 4.97 %RANDOM
Rwork0.1691 ---
obs0.1703 91941 66.6 %-
Displacement parametersBiso mean: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.7266 Å20 Å20.4616 Å2
2---0.9673 Å20 Å2
3---1.6939 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.256→18.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 49 521 4474
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0138089HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2214637HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2379SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1262HARMONIC5
X-RAY DIFFRACTIONt_it8089HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.38
X-RAY DIFFRACTIONt_other_torsion3.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion532SEMIHARMONIC5
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_contact8188SEMIHARMONIC4
LS refinement shellResolution: 1.26→1.32 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2623 -4.35 %
Rwork0.2786 1759 -
all0.2779 1839 -
obs--9.35 %
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)
11.46330.20810.46710.19360.00780.2110.1779-0.4877-0.09770.0023-0.1160.00410.0429-0.1304-0.0619-0.0539-0.0894-0.00570.15460.076-0.050111.1145-2.875833.7716
20.35970.12960.01880.04190.05960.27750.0405-0.0397-0.0225-0.0121-0.0278-0.027-0.0057-0.0159-0.0127-0.0006-0.00270.0108-0.04450.00020.040518.14624.3628.3415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|281 A|493 - A|521 }A31 - 281
2X-RAY DIFFRACTION1{ A|31 - A|281 A|493 - A|521 }A493 - 521
3X-RAY DIFFRACTION2{ A|282 - A|492 }A282 - 492

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