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- PDB-5o37: Pseudomonas stutzeri PtxB in complex with methylphosphonate (MPn)... -

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Basic information

Entry
Database: PDB / ID: 5o37
TitlePseudomonas stutzeri PtxB in complex with methylphosphonate (MPn) to 1.37 A resolution
ComponentsProbable phosphite transport system-binding protein PtxB
KeywordsTRANSPORT PROTEIN / phosphite / ABC transporters / marine bacteria / PBP / SBP
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYLPHOSPHONIC ACID ESTER GROUP / Probable phosphite transport system-binding protein PtxB
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBisson, C. / Hitchcock, A.
CitationJournal: Nat Commun / Year: 2017
Title: The molecular basis of phosphite and hypophosphite recognition by ABC-transporters.
Authors: Bisson, C. / Adams, N.B.P. / Stevenson, B. / Brindley, A.A. / Polyviou, D. / Bibby, T.S. / Baker, P.J. / Hunter, C.N. / Hitchcock, A.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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: Probable phosphite transport system-binding protein PtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2692
Polymers30,1731
Non-polymers961
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA analysis also suggests a monomeric assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint3 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.800, 39.120, 63.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-615-

HOH

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Components

#1: Protein Probable phosphite transport system-binding protein PtxB


Mass: 30173.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal 6x His-tag / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69052
#2: Chemical ChemComp-GB / METHYLPHOSPHONIC ACID ESTER GROUP


Mass: 96.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MMT buffer pH 4 and 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.37→37.61 Å / Num. obs: 59851 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 1 / Rpim(I) all: 0.022 / Net I/σ(I): 16.8
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2940 / CC1/2: 0.485 / Rpim(I) all: 0.615 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→37.61 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.75 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17723 2974 5 %RANDOM
Rwork0.13695 ---
obs0.13893 56823 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.72 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.37→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 5 225 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192090
X-RAY DIFFRACTIONr_bond_other_d0.0030.021956
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9782843
X-RAY DIFFRACTIONr_angle_other_deg1.49434547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28124.78794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53515356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4061511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212346
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02405
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_it2.4981.6891053
X-RAY DIFFRACTIONr_mcbond_other3.6271.6861052
X-RAY DIFFRACTIONr_mcangle_it2.8322.5341317
X-RAY DIFFRACTIONr_mcangle_other3.5932.541318
X-RAY DIFFRACTIONr_scbond_it8.3232.2441037
X-RAY DIFFRACTIONr_scbond_other8.3192.2431038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7313.1181522
X-RAY DIFFRACTIONr_long_range_B_refined5.5821.7262188
X-RAY DIFFRACTIONr_long_range_B_other5.47521.1592147
X-RAY DIFFRACTIONr_rigid_bond_restr10.68434045
X-RAY DIFFRACTIONr_sphericity_free25.2995169
X-RAY DIFFRACTIONr_sphericity_bonded22.96954058
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 213 -
Rwork0.3 4160 -
obs--98.98 %

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