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- PDB-8cko: PBP AccA from A.tumefaciens C58 in complex with agrocinopine C-like -

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Basic information

Entry
Database: PDB / ID: 8cko
TitlePBP AccA from A.tumefaciens C58 in complex with agrocinopine C-like
ComponentsABC transporter substrate-binding protein
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
: / : / 2-O-phosphono-alpha-D-glucopyranose / 2-O-phosphono-beta-D-glucopyranose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.421 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 16, 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)58,3835
Polymers57,1781
Non-polymers1,2054
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint7 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.680, 108.949, 113.240
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-1126-

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: 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_002508
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
#3: 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_002508
#4: 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).
Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002507
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / 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: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.42→78.51 Å / Num. obs: 74582 / % possible obs: 81.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 20.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.1
Reflection shellResolution: 1.42→1.53 Å / Rmerge(I) obs: 2.059 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3729 / CC1/2: 0.422

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.421→78.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.075 / SU Rfree Cruickshank DPI: 0.073
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 3841 5.15 %RANDOM
Rwork0.1623 ---
obs0.164 74582 81.5 %-
Displacement parametersBiso mean: 24.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.4206 Å20 Å20 Å2
2--0.7673 Å20 Å2
3---0.6533 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.421→78.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 38 452 4453
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118082HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114604HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2366SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1231HARMONIC5
X-RAY DIFFRACTIONt_it8082HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.12
X-RAY DIFFRACTIONt_other_torsion14.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion528SEMIHARMONIC5
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_contact7581SEMIHARMONIC4
LS refinement shellResolution: 1.421→1.5 Å
RfactorNum. reflection% reflection
Rfree0.337 -3.62 %
Rwork0.2571 1438 -
obs--10.93 %
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)
11.58051.1636-0.41521.14060.21970.80760.0998-0.2514-0.21610.133-0.1515-0.1773-0.02480.21270.0517-0.0489-0.0215-0.04410.04150.0747-0.008531.194720.4116153.609
20.87970.2582-0.01040.43940.25240.8431-0.01780.0311-0.20650.0278-0.0638-0.03420.06370.0030.0816-0.04120.00420.0239-0.0355-0.01270.050215.4787.7982137.793
30.88740.48860.0360.66990.35190.7424-0.0078-0.0492-0.16320.0488-0.0638-0.06550.02360.06520.0716-0.05050.00640.0047-0.02460.02690.026221.27214.7004143.216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|30 - A|240 }A30 - 240
2X-RAY DIFFRACTION2{ A|241 - A|521 A|601 - A|601 }A241 - 521
3X-RAY DIFFRACTION2{ A|241 - A|521 A|601 - A|601 }A601
4X-RAY DIFFRACTION3{ C|3 - C|3 A|701 - A|1152 }C3
5X-RAY DIFFRACTION3{ C|3 - C|3 A|701 - A|1152 }A701 - 1152

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