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- PDB-8c6u: PBP AccA-G145YG440Q mutant from A. tumefaciens Bo542 in apoform 4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8c6u
TitlePBP AccA-G145YG440Q mutant from A. tumefaciens Bo542 in apoform 4
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.843 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

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)56,9129
Polymers56,3811
Non-polymers5328
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint11 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.258, 60.013, 181.236
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: 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, AcNH4, Na citrate

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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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.84→45 Å / Num. obs: 51418 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.997 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 1.84→1.89 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 3718 / CC1/2: 0.126

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.843→24.12 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 1531 -RANDOM
Rwork0.2344 ---
obs0.2368 31943 62.5 %-
Displacement parametersBiso mean: 30.02 Å2
Baniso -1Baniso -2Baniso -3
1-8.2447 Å20 Å20 Å2
2---6.3481 Å20 Å2
3----1.8966 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 1.843→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 35 259 4204
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097946HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0514351HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2330SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1234HARMONIC5
X-RAY DIFFRACTIONt_it7946HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion516SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6935SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion15.42
LS refinement shellResolution: 1.843→1.95 Å
RfactorNum. reflection% reflection
Rfree0.3333 31 -
Rwork0.2635 --
obs--8.33 %
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)
10.2175-0.0523-0.33540.84030.25640.21080.04150.02040.00480.0204-0.02390.00090.00480.0009-0.01760.1712-0.0060.01-0.12850.008-0.084220.863921.1988-28.8842
20.0131-0.3575-0.40750.9942-0.10991.0953-0.07630.00850.11290.00850.0717-0.07490.1129-0.07490.00470.0958-0.04180.0382-0.1144-0.0275-0.04636.84071.484-12.1806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|281 }A31 - 281
2X-RAY DIFFRACTION1{ A|493 - A|521 }A493 - 521
3X-RAY DIFFRACTION2{ A|282 - A|492 }A282 - 492

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