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- PDB-8ci6: PBP AccA from A. vitis S4 in complex with D-glucose-2-phosphate (G2P) -

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Basic information

Entry
Database: PDB / ID: 8ci6
TitlePBP AccA from A. vitis S4 in complex with D-glucose-2-phosphate (G2P)
ComponentsABC transporter substrate binding protein (Agrocinopine)
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / 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 / ABC transporter substrate binding protein (Agrocinopine)
Similarity search - Component
Biological speciesAllorhizobium ampelinum S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 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 8, 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 (Agrocinopine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1733
Polymers56,6521
Non-polymers5202
Water11,674648
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20110 Å2
Unit cell
Length a, b, c (Å)47.300, 61.060, 152.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter substrate binding protein (Agrocinopine)


Mass: 56652.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allorhizobium ampelinum S4 (bacteria) / Gene: accA / Production host: Escherichia coli (E. coli) / References: UniProt: B9JXG4
#2: 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 / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 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 / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.199→47.66 Å / Num. obs: 138637 / % possible obs: 99.7 % / Redundancy: 11.8 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.48
Reflection shellResolution: 1.2→1.27 Å / Rmerge(I) obs: 0.881 / Num. unique obs: 21841 / CC1/2: 0.707

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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: 1.199→47.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU R Cruickshank DPI: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.044 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.043
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 6931 5 %RANDOM
Rwork0.1781 ---
obs0.179 138593 99.7 %-
Displacement parametersBiso mean: 24.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.7645 Å20 Å20 Å2
2--2.8087 Å20 Å2
3----2.0442 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.199→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 17 650 4476
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0147815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2214148HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2289SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1213HARMONIC5
X-RAY DIFFRACTIONt_it7815HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.62
X-RAY DIFFRACTIONt_other_torsion15.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion517SEMIHARMONIC5
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_contact7848SEMIHARMONIC4
LS refinement shellResolution: 1.2→1.21 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4132 138 4.98 %
Rwork0.3831 2634 -
all0.3846 2772 -
obs--89.3 %
Refinement TLS params.Method: refined / Origin x: 17.641 Å / Origin y: -1.3259 Å / Origin z: -19.1493 Å
111213212223313233
T-0.0037 Å2-0.0018 Å2-0.0102 Å2--0.0554 Å2-0.0048 Å2---0.11 Å2
L0.1998 °20.1047 °2-0.0025 °2-1.1335 °2-0.1842 °2--0.1933 °2
S0.021 Å °-0.0627 Å °0.0113 Å °0.371 Å °-0.0287 Å °-0.0268 Å °-0.0591 Å °-0.0012 Å °0.0078 Å °
Refinement TLS groupSelection details: { A|* }

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