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- PDB-8ch2: PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate... -

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Basic information

Entry
Database: PDB / ID: 8ch2
TitlePBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P)
ComponentsAccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-beta-L-arabinopyranose
Function and homology information
Biological speciesAgrobacterium vitis S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 Å
AuthorsMorera, S. / Deicsics, G. / 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 6, 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

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Assembly

Deposited unit
A: AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1754
Polymers56,6521
Non-polymers5223
Water10,088560
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area20120 Å2
Unit cell
Length a, b, c (Å)47.080, 61.030, 152.810
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 AccA


Mass: 56652.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis S4 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Sugar ChemComp-LAO / 2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-alpha-L-arabinose / 2-O-phosphono-L-arabinose / 2-O-phosphono-arabinose


Type: L-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-VDF / 2-O-phosphono-beta-L-arabinopyranose / 2-O-phosphono-beta-L-arabinose / 2-O-phosphono-L-arabinose / 2-O-phosphono-arabinose / [(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate


Type: L-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P
#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.: 560 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / 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 2 / Wavelength: 0.983997 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983997 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 86791 / % possible obs: 99.8 % / Redundancy: 6.24 % / Biso Wilson estimate: 18.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.57
Reflection shellResolution: 1.4→1.49 Å / Rmerge(I) obs: 0.881 / Num. unique obs: 13746 / CC1/2: 0.964

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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: 1.404→14.14 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.061
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 4334 5 %RANDOM
Rwork0.1731 ---
obs0.1741 86686 99.9 %-
Displacement parametersBiso mean: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.1726 Å20 Å20 Å2
2--1.8262 Å20 Å2
3----0.6536 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.404→14.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 19 560 4399
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117830HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1614170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2288SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1211HARMONIC5
X-RAY DIFFRACTIONt_it7830HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.29
X-RAY DIFFRACTIONt_other_torsion14.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion516SEMIHARMONIC5
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_contact7661SEMIHARMONIC4
LS refinement shellResolution: 1.404→1.41 Å
RfactorNum. reflection% reflection
Rfree0.2541 -5.02 %
Rwork0.2301 1647 -
obs--95.83 %
Refinement TLS params.Method: refined / Origin x: 17.641 Å / Origin y: -1.3259 Å / Origin z: -19.1493 Å
111213212223313233
T0.0231 Å20.0043 Å20.0056 Å2--0.0481 Å2-0.0017 Å2---0.067 Å2
L0.2914 °20.1913 °2-0.0263 °2-1.3995 °2-0.0051 °2--0.2893 °2
S0.0412 Å °-0.0999 Å °0.0083 Å °0.4428 Å °-0.0303 Å °-0.0022 Å °0.0029 Å °0.0265 Å °-0.0109 Å °
Refinement TLS groupSelection details: { A|* }

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