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- PDB-8c6w: PBP AccA from A. tumefaciens Bo542 in apoform 1 -

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Basic information

Entry
Database: PDB / ID: 8c6w
TitlePBP AccA from A. tumefaciens Bo542 in apoform 1
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / solute binding protein
Function / homologydipeptide transport / 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 / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / Agrocinopine utilization periplasmic binding protein AccA
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorera, S. / Vigouroux, A. / Legrand, P.
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 12, 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: Agrocinopine utilization periplasmic binding protein AccA
B: Agrocinopine utilization periplasmic binding protein AccA


Theoretical massNumber of molelcules
Total (without water)112,5882
Polymers112,5882
Non-polymers00
Water3,045169
1
A: Agrocinopine utilization periplasmic binding protein AccA


Theoretical massNumber of molelcules
Total (without water)56,2941
Polymers56,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agrocinopine utilization periplasmic binding protein AccA


Theoretical massNumber of molelcules
Total (without water)56,2941
Polymers56,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.723, 100.568, 116.016
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agrocinopine utilization periplasmic binding protein AccA


Mass: 56293.750 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.24 %
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 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.8→49 Å / Num. obs: 27072 / % possible obs: 85.7 % / Redundancy: 12 % / CC1/2: 0.994 / Rmerge(I) obs: 0.343 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 1.622 / Num. unique obs: 1963 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.03 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.451
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 1159 -RANDOM
Rwork0.2276 ---
obs0.2295 23246 85.9 %-
Displacement parametersBiso mean: 50.45 Å2
Baniso -1Baniso -2Baniso -3
1-6.8009 Å20 Å20 Å2
2---5.435 Å20 Å2
3----1.3658 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 0 169 7975
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0058010HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7610882HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2734SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1358HARMONIC5
X-RAY DIFFRACTIONt_it8010HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1028SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6361SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion16.58
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.4169 18 -
Rwork0.3126 --
obs0.3167 465 25.16 %
Refinement TLS params.

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)
10.9106-0.2212-0.19521.9130.38091.55840.0361-0.02780.0219-0.0278-0.0482-0.06610.0219-0.06610.0121-0.0113-0.0344-0.0411-0.1550.0343-0.0523-6.052918.5439-31.0745
20.95080.43890.41922.57360.59651.9213-0.00190.0077-0.06860.0077-0.0158-0.0408-0.0686-0.04080.0177-0.07890.03660.0681-0.1720.0411-0.0557-5.920436.6211-84.9593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A31 - 521
2X-RAY DIFFRACTION2{ B|* }B31 - 521

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