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- PDB-8cb9: PBP AccA from A. tumefaciens Bo542 in complex with D-Glucose-2-ph... -

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Basic information

Entry
Database: PDB / ID: 8cb9
TitlePBP AccA from A. tumefaciens Bo542 in complex with D-Glucose-2-phosphate
ComponentsAgrocinopine utilization periplasmic binding protein AccA
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 / Agrocinopine utilization periplasmic binding protein AccA
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionJan 25, 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)55,8543
Polymers55,3341
Non-polymers5202
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.922, 59.183, 183.329
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 Agrocinopine utilization periplasmic binding protein AccA


Mass: 55333.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: few amino acids were not visible in the electron density maps
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: 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
#3: 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: isolated from a natural source / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp2PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
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 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.79→91.665 Å / Num. obs: 32306 / % possible obs: 91.9 % / Redundancy: 12.58 % / Biso Wilson estimate: 31.73 Å2
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.375 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.0216 / Rrim(I) all: 0.0772 / AbsDiff over sigma anomalous: 0.705 / Baniso tensor eigenvalue 1: 80 Å2 / Baniso tensor eigenvalue 2: 28.5 Å2 / Baniso tensor eigenvalue 3: 25.4 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.384 Å / Aniso diffraction limit 2: 1.769 Å / Aniso diffraction limit 3: 1.74 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 16.28 / Num. measured all: 406524 / Orthogonalization convention: pdb / % possible anomalous: 91.8 / % possible ellipsoidal: 91.9 / % possible ellipsoidal anomalous: 91.8 / % possible spherical: 71.7 / % possible spherical anomalous: 70.4 / Redundancy anomalous: 6.73
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.633-91.66411.520.034350.071858918589161416140.999-0.6180.01050.03590.63610099.910099.91006.8999.9
4.425-5.63313.060.040848.912111821118161716170.999-0.4270.01170.04250.6621001001001001007.25100
3.84-4.42512.870.044143.862076720767161416140.999-0.4290.01270.0460.6810099.910099.91007.0399.9
3.477-3.8412.460.056134.72014020140161616160.999-0.290.01660.05850.7321001001001001006.76100
3.222-3.47713.160.0727.982126721267161616160.999-0.1530.02020.07290.7511001001001001007.09100
3.026-3.22213.630.087722.132200222002161416140.998-0.0570.02460.09120.7481001001001001007.3100
2.869-3.02613.880.112917.592243422434161616160.997-0.2420.03130.11720.7141001001001001007.37100
2.741-2.86914.050.149613.622269822698161516150.997-0.1670.04130.15530.7271001001001001007.47100
2.633-2.74113.060.17211.462108621086161516150.996-0.0070.04940.17910.7471001001001001006.92100
2.539-2.63313.40.22079.192165721657161616160.994-0.1140.06260.22950.70699.999.799.999.799.97.0699.7
2.453-2.53912.960.26747.712092020920161416140.99-0.0160.07730.27850.72194.593.594.593.594.56.8393.5
2.372-2.45313.70.30726.912213422134161616160.99-0.0770.0860.31920.69690.590.190.589.289.97.1990.1
2.299-2.37213.940.33116.592251222512161516150.986-0.0550.09180.34390.71788.888.988.88484.27.3488.9
2.231-2.29914.180.375662290922909161616160.983-0.0240.10360.38990.71891.491.691.480.8817.4791.6
2.166-2.23114.440.45465.062331823318161516150.974-0.050.12360.47130.67793.793.793.776.976.87.5993.7
2.106-2.16614.460.54434.282334923349161516150.9730.0220.1480.56420.69894.694.894.671.771.57.694.8
2.046-2.10612.490.63453.462017020170161516150.953-0.0170.18580.66150.71194.694.994.666.465.56.5594.9
1.986-2.04610.490.6972.881694316943161516150.897-0.0280.22180.73260.6919494.29457.957.15.594.2
1.924-1.9867.740.81561.971250512505161616160.775-0.0440.30360.8740.69289.89089.849.848.54.0690
1.79-1.9246.191.22141.211000610006161616160.527-0.1020.50781.33060.65448.649.248.618.817.43.349.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
autoPROCdata processing
autoPROCFeb 5, 2021data processing
autoPROC0.7.4data scaling
autoPROC2.3.63data processing
autoPROCdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8C6R

8c6r


Resolution: 1.79→23.55 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 1.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.235 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.192
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1583 4.9 %RANDOM
Rwork0.2279 ---
obs0.23 32278 71.7 %-
Displacement parametersBiso mean: 45.19 Å2
Baniso -1Baniso -2Baniso -3
1-5.2976 Å20 Å20 Å2
2--0.6329 Å20 Å2
3----5.9304 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.79→23.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3865 0 16 174 4055
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097843HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0514179HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2304SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1222HARMONIC5
X-RAY DIFFRACTIONt_it7843HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion15.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion515SEMIHARMONIC5
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_contact6640SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.88 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4294 -6.5 %
Rwork0.3105 604 -
all0.318 646 -
obs--10.77 %
Refinement TLS params.

L11: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL12 (°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)
1-0.07241.23240.1439-0.24612.80670.1843-0.04230.1065-0.0604-0.122-0.01710.37420.1718-0.06230.14580.0401-0.133-0.0248-0.0087-0.0672-3.1488-13.751429.436
20.69681.762100.01134.5322-0.2551-0.1588-0.0136-0.21850.0271-0.0757-0.5442-0.36240.22790.20290.0736-0.1246-0.0054-0.0349-0.0989-15.4659-1.165812.6101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|282 }A31 - 282
2X-RAY DIFFRACTION2{ A|283 - A|521 }A283 - 521

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