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- PDB-6hlx: Structure of the PBP AgaA in complex with agropinic acid from A.t... -

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Basic information

Entry
Database: PDB / ID: 6hlx
TitleStructure of the PBP AgaA in complex with agropinic acid from A.tumefacien R10
ComponentsAgaA
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / ABC transporter
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / agropinic acid / DI(HYDROXYETHYL)ETHER / AgaA
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AgaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,38738
Polymers54,4591
Non-polymers2,92837
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-149 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.260, 89.260, 285.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AgaA / Peptide ABC transporter substrate-binding protein / Peptide/nickel transport system substrate-binding protein


Mass: 54459.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: agaA, A6U90_18825, At1D1609_52290 / Production host: Escherichia coli (E. coli) / References: UniProt: O50260

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Non-polymers , 9 types, 507 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-G9Z / agropinic acid


Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 1.8 M AS, 0.1 M Mes pH 6.5, 0.2 M Zn acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→52.48 Å / Num. obs: 82437 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 26.82 Å2 / Rsym value: 0.132 / Net I/σ(I): 19.2
Reflection shellResolution: 1.65→1.74 Å / Rsym value: 2.052

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1Q and 1DPP

3f1q

1dpp


Resolution: 1.65→52.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.067
RfactorNum. reflection% reflectionSelection details
Rfree0.174 4109 5 %RANDOM
Rwork0.156 ---
obs0.157 82180 99.4 %-
Displacement parametersBiso mean: 29.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.4528 Å20 Å20 Å2
2--1.4528 Å20 Å2
3----2.9056 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.65→52.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 167 470 4474
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014096HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975521HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1393SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes687HARMONIC5
X-RAY DIFFRACTIONt_it4096HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion16.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion524SEMIHARMONIC5
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_contact5112SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.66 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3878 -4.93 %
Rwork0.3383 1563 -
all0.3407 1644 -
obs--77.95 %
Refinement TLS params.Method: refined / Origin x: 80.1144 Å / Origin y: -31.7036 Å / Origin z: 1.2197 Å
111213212223313233
T-0.1073 Å20.0099 Å2-0.0119 Å2--0.1256 Å2-0.0415 Å2---0.1294 Å2
L0.6565 °20.0603 °2-0.1845 °2-0.5201 °20.167 °2--0.4228 °2
S-0.005 Å °-0.0338 Å °0.0187 Å °-0.0153 Å °0.0067 Å °-0.0188 Å °-0.0563 Å °0.0045 Å °-0.0018 Å °
Refinement TLS groupSelection details: { A|25 - A|169 A|175 - A|315 A|322 - A|512 }

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