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- PDB-6hly: Structure in P212121 form of the PBP AgtB in complex with agropin... -

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Basic information

Entry
Database: PDB / ID: 6hly
TitleStructure in P212121 form of the PBP AgtB in complex with agropinic acid from A.tumefacien R10
ComponentsAgropine permease
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / ABC transporter
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / agropinic acid / :
Function and homology information
Biological speciesAgrobacterium tumefaciens LBA4213
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMorera, S. / Marty, L. / Vigouroux, A.
CitationJournal: Biochem. J. / Year: 2019
Title: Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogenAgrobacterium tumefaciens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Pelissier, F. / Meyer, T. / Lavire, C. / Dessaux, Y. / Morera, S.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agropine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,14211
Polymers37,2921
Non-polymers85010
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint21 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.860, 108.930, 64.440
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 Agropine permease


Mass: 37291.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens LBA4213 (Ach5) (bacteria)
Gene: agtB, X971_5368 / Production host: Escherichia coli (E. coli) / References: UniProt: W8FRA6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-G9Z / agropinic acid


Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.92 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4K, 0.1 M Tris pH 8.5, 0.2 M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 57167 / % possible obs: 99.2 % / Redundancy: 5 % / Biso Wilson estimate: 22.46 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.4→1.48 Å / Rsym value: 0.951

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9G

5l9g


Resolution: 1.4→20.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.067
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2858 5 %RANDOM
Rwork0.182 ---
obs0.184 57146 99.2 %-
Displacement parametersBiso mean: 28.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.7609 Å20 Å20 Å2
2---0.8713 Å20 Å2
3---1.6322 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.4→20.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 56 291 2816
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012604HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033532HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d859SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes438HARMONIC5
X-RAY DIFFRACTIONt_it2604HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion16.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion331SEMIHARMONIC5
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_contact3370SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.41 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2571 -4.99 %
Rwork0.2808 1086 -
all0.2796 1143 -
obs--85.41 %
Refinement TLS params.Method: refined / Origin x: 53.6781 Å / Origin y: 11.7804 Å / Origin z: 78.3646 Å
111213212223313233
T-0.0566 Å20.0035 Å2-0.0049 Å2--0.078 Å2-0.0029 Å2---0.0722 Å2
L0.8522 °2-0.1136 °2-0.0622 °2-1.6727 °2-0.162 °2--0.4774 °2
S0.0328 Å °-0.0281 Å °-0.1158 Å °-0.1081 Å °-0.0154 Å °0.0216 Å °0.0761 Å °0.0156 Å °-0.0174 Å °
Refinement TLS groupSelection details: { A|* }

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