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- PDB-6esv: Structure of the phosphate-bound form of AioX from Rhizobium sp. ... -

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Basic information

Entry
Database: PDB / ID: 6esv
TitleStructure of the phosphate-bound 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 / PHOSPHATE ION / 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 / SAD / Resolution: 1.78 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 24, 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)31,5222
Polymers31,4271
Non-polymers951
Water2,288127
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-10 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.544, 124.544, 48.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 31426.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a Se-Met labeled protein which is why MET residues are replaced with MSE. Two residues, K230 and R173 (or K250 and R193 as numbered in the PDB file to reflect the protein numbering ...Details: This is a Se-Met labeled protein which is why MET residues are replaced with MSE. Two residues, K230 and R173 (or K250 and R193 as numbered in the PDB file to reflect the protein numbering after the transport signal peptide was removed) were modeled as Alanines due to the disorder for the side chain. Similarly, residues 37 and 38 (57 and 58) were not modeled due to disorder.
Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aioX, NT26_p10026 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NML6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.49 M NaH2PO4 and 0.91 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.78→88.07 Å / Num. obs: 36718 / % possible obs: 99.8 % / Redundancy: 16.4 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→88.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.67 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22038 1701 4.8 %RANDOM
Rwork0.19041 ---
obs0.19189 33414 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.742 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.78→88.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 5 127 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192084
X-RAY DIFFRACTIONr_bond_other_d0.0020.021967
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.9662829
X-RAY DIFFRACTIONr_angle_other_deg1.07634502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41523.26598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44215323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212384
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
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_it3.0252.8441047
X-RAY DIFFRACTIONr_mcbond_other3.0222.841046
X-RAY DIFFRACTIONr_mcangle_it4.0474.2431307
X-RAY DIFFRACTIONr_mcangle_other4.0464.2461308
X-RAY DIFFRACTIONr_scbond_it4.7593.3391035
X-RAY DIFFRACTIONr_scbond_other4.7643.3461032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.544.8181516
X-RAY DIFFRACTIONr_long_range_B_refined7.75823.5832447
X-RAY DIFFRACTIONr_long_range_B_other7.77223.3922405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 116 -
Rwork0.288 2119 -
obs--84.37 %

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