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- PDB-6esk: Structure of the apo form of AioX from Rhizobium sp. str. NT-26 -

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Basic information

Entry
Database: PDB / ID: 6esk
TitleStructure of the apo form of AioX from Rhizobium sp. str. NT-26
ComponentsPutative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
KeywordsSIGNALING PROTEIN / Periplasmic-binding protein / Arsenic / arsenite-binding / Rhizobium NT-26
Function / homologyABC transporter, phosphonate, periplasmic substrate-binding protein / Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
Function and homology information
Biological speciesRhizobium sp. NT-26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDjordjevic, S. / Badilla, C. / Cole, A. / Santini, J.
Funding support Chile, United Kingdom, 2items
OrganizationGrant numberCountry
CONICYT Chile
Biotechnology and Biological Sciences Research CouncilBB/N012674/1 United Kingdom
CitationJournal: Sci Rep / Year: 2018
Title: A new family of periplasmic-binding proteins that sense arsenic oxyanions.
Authors: Badilla, C. / Osborne, T.H. / Cole, A. / Watson, C. / Djordjevic, S. / Santini, J.M.
History
DepositionOct 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 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: Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7754
Polymers29,4981
Non-polymers2763
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-2 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.877, 124.877, 47.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

#1: Protein Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX


Mass: 29498.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The two N-terminal residues are a cloning artifact.
Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aioX, NT26_p10026 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NML6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M sodium malonate and 0.1 M Bis-Tris propane, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→44.59 Å / Num. obs: 38474 / % possible obs: 98.9 % / Redundancy: 12.8 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESV

6esv


Resolution: 1.75→88.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.909 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21115 1864 4.9 %RANDOM
Rwork0.18737 ---
obs0.18854 36519 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.719 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→88.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 18 80 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192132
X-RAY DIFFRACTIONr_bond_other_d0.0060.022025
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9622887
X-RAY DIFFRACTIONr_angle_other_deg1.08834638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68123.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6911520
X-RAY DIFFRACTIONr_chiral_restr0.1330.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022427
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.932.5441060
X-RAY DIFFRACTIONr_mcbond_other2.8862.5411059
X-RAY DIFFRACTIONr_mcangle_it4.0463.7981325
X-RAY DIFFRACTIONr_mcangle_other4.0523.8021326
X-RAY DIFFRACTIONr_scbond_it4.8123.2071072
X-RAY DIFFRACTIONr_scbond_other4.8113.2071072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4124.5451563
X-RAY DIFFRACTIONr_long_range_B_refined8.9821.3962413
X-RAY DIFFRACTIONr_long_range_B_other8.97821.4152414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 127 -
Rwork0.383 2314 -
obs--86.47 %

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