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- PDB-8cdo: PBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agr... -

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Basic information

Entry
Database: PDB / ID: 8cdo
TitlePBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agrocinopine C-like
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology
Function and homology information


dipeptide 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
: / : / 2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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
DepositionJan 31, 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)58,59517
Polymers56,3811
Non-polymers2,21416
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint40 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.116, 122.116, 122.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Agrocinopine utilization periplasmic binding protein AccA


Mass: 56380.828 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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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: isolated from a genetically manipulated source
Details: Phosphodiester of D-beta-glucose (BNX) and sucrose (GLC-FRU).
References: BIRD: PRD_002548
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
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-BNX / 2-O-phosphono-beta-D-glucopyranose / 2-O-phosphono-beta-D-glucose / 2-O-phosphono-D-glucose / 2-O-phosphono-glucose


Type: D-saccharide, beta linking, Oligosaccharide / Class: Nutrient / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
Details: Phosphodiester of D-beta-glucose (BNX) and sucrose (GLC-FRU).
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002548
#8: Sugar ChemComp-ALX / 2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-alpha-D-glucose / 2-O-phosphono-D-glucose / 2-O-phosphono-glucose


Type: D-saccharide, alpha linking, Oligosaccharide / Class: Nutrient / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
Details: Phosphodiester of D-alpha-glucose (ALX) and sucrose (GLC-FRU).
References: BIRD: PRD_002547
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 628 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsIsomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of ...Isomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of sucrose and D-glucose joined via a phosphodiester linkage.
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: 2.82 Å3/Da / Density % sol: 56.36 %
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: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.32→86.3 Å / Num. obs: 135341 / % possible obs: 95.6 % / Redundancy: 40.9 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.3
Reflection shellResolution: 1.32→1.36 Å / Rmerge(I) obs: 3.27 / Num. unique obs: 6758 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→19.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.042 / SU Rfree Blow DPI: 0.044 / SU Rfree Cruickshank DPI: 0.042
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1678 6645 4.91 %RANDOM
Rwork0.147 ---
obs0.148 135283 95.6 %-
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.32→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 104 616 4518
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0128200HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1714832HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2462SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1274HARMONIC5
X-RAY DIFFRACTIONt_it8200HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.89
X-RAY DIFFRACTIONt_other_torsion13.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion535SEMIHARMONIC5
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_contact8404SEMIHARMONIC4
LS refinement shellResolution: 1.32→1.34 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2572 137 5.06 %
Rwork0.247 2569 -
all0.2475 2706 -
obs--42.33 %
Refinement TLS params.Method: refined / Origin x: 8.9353 Å / Origin y: 29.0439 Å / Origin z: -6.8148 Å
111213212223313233
T-0.0599 Å20.0064 Å20.0089 Å2--0.0658 Å20.009 Å2---0.0642 Å2
L0.3847 °2-0.1256 °2-0.0011 °2-0.2428 °20.0781 °2--0.2704 °2
S-0.0138 Å °-0.0275 Å °0.0018 Å °-0.0105 Å °-0.001 Å °0.0033 Å °-0.0067 Å °-0.0026 Å °0.0148 Å °
Refinement TLS groupSelection details: { A|* }

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