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- PDB-8c75: PBP AccA from A. tumefaciens Bo542 in apoform 3 -

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Basic information

Entry
Database: PDB / ID: 8c75
TitlePBP AccA from A. tumefaciens Bo542 in apoform 3
ComponentsAgrocinopine utilization periplasmic binding protein AccA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / solute binding protein
Function / homology
Function and homology information


peptide 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 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
B: Agrocinopine utilization periplasmic binding protein AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9758
Polymers112,5882
Non-polymers3876
Water13,061725
1
A: Agrocinopine utilization periplasmic binding protein AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4673
Polymers56,2941
Non-polymers1732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agrocinopine utilization periplasmic binding protein AccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5085
Polymers56,2941
Non-polymers2144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.99, 182.075, 58.606
Angle α, β, γ (deg.)90, 94.09, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 731 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.62 %
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: 1.66→49.19 Å / Num. obs: 113578 / % possible obs: 74 % / Redundancy: 5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.3
Reflection shellResolution: 1.66→1.71 Å / Rmerge(I) obs: 1.117 / Num. unique obs: 7440 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.673→49.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.278 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 4223 -RANDOM
Rwork0.2194 ---
obs0.2212 83458 74.1 %-
Displacement parametersBiso mean: 32.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.6436 Å20 Å20.0692 Å2
2---0.0923 Å20 Å2
3---1.736 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.673→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 24 725 8557
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115783HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0928537HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4628SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2458HARMONIC5
X-RAY DIFFRACTIONt_it15783HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1031SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15233SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.46
X-RAY DIFFRACTIONt_other_torsion15.96
LS refinement shellResolution: 1.673→1.76 Å
RfactorNum. reflection% reflection
Rfree0.3163 64 -
Rwork0.293 --
obs--10.73 %
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)
10.6783-0.5999-0.10991.21810.35781.46390.0416-0.11810.0304-0.11810.02030.03740.03040.0374-0.0619-0.1279-0.0090.0019-0.10810.0089-0.066320.67148.9487-47.4818
23.31170.1399-1.65192.74780.15912.9439-0.39430.35510.67980.35510.14980.13770.67980.13770.24450.04550.06560.0059-0.067-0.02420.027632.2018-8.2928-27.3329
30.745-0.33260.39390.9229-0.37131.7421-0.0175-0.0913-0.0495-0.0913-0.0422-0.0027-0.0495-0.00270.0596-0.13840.00580.0115-0.1176-0.0012-0.04778.940842.1987-19.1147
43.5248-1.24422.30662.7128-0.9883.6384-0.47790.2656-0.68570.2656-0.0633-0.0242-0.6857-0.02420.5413-0.0330.0126-0.0865-0.11010.0010.0868-5.196859.3229-1.0194
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
4X-RAY DIFFRACTION3{ B|31 - B|281 }B31 - 281
5X-RAY DIFFRACTION3{ B|493 - B|521 }B493 - 521
6X-RAY DIFFRACTION4{ B|282 - B|492 }B282 - 492

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