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- PDB-8ed5: Crystal structure of loop deletion AioX mutant from Pseudorhizobi... -

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Basic information

Entry
Database: PDB / ID: 8ed5
TitleCrystal structure of loop deletion AioX mutant from Pseudorhizobium sp. str. NT-26
ComponentsPutative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX
KeywordsSIGNALING PROTEIN
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 speciesPseudorhizobium banfieldiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMaher, M.J. / Poddar, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Investigating the interaction of the periplasmic arsenite-binding protein, AioX with the sensor histidine kinase, AioS from Pseudorhizobium banfieldii sp. str. NT-26
Authors: Maher, M.J. / Poddar, N.
History
DepositionSep 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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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)33,3693
Polymers33,1841
Non-polymers1842
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.155, 125.155, 47.415
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-503-

HOH

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Components

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


Mass: 33184.387 Da / Num. of mol.: 1 / Mutation: F57A, deletion of L58-N60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEG 3350,0.2 M sodium malonate, 0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.79→47.4 Å / Num. obs: 35865 / % possible obs: 99.6 % / Redundancy: 26.4 % / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 1.79→1.83 Å / Num. unique obs: 1979 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ESK

6esk


Resolution: 1.79→44.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.433 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19787 1772 5 %RANDOM
Rwork0.1846 ---
obs0.18527 33961 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.638 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0 Å2
2--0.7 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.79→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 12 162 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132204
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172119
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6493000
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5814864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1619.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7361527
X-RAY DIFFRACTIONr_chiral_restr0.0540.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
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_it1.6663.0061077
X-RAY DIFFRACTIONr_mcbond_other1.6492.9991075
X-RAY DIFFRACTIONr_mcangle_it2.6534.5021354
X-RAY DIFFRACTIONr_mcangle_other2.644.5011354
X-RAY DIFFRACTIONr_scbond_it2.1023.321125
X-RAY DIFFRACTIONr_scbond_other2.1013.3211126
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4854.861633
X-RAY DIFFRACTIONr_long_range_B_refined10.22435.6232485
X-RAY DIFFRACTIONr_long_range_B_other10.22635.5752482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 125 -
Rwork0.277 2299 -
obs--93.23 %

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