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- PDB-5o2j: Pseudomonas stutzeri PtxB in complex with phosphite to 1.52 A res... -

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Basic information

Entry
Database: PDB / ID: 5o2j
TitlePseudomonas stutzeri PtxB in complex with phosphite to 1.52 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
PHOSPHONATE / Probable phosphite transport system-binding protein PtxB
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBisson, C. / Hitchcock, A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000265/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011305/1 United Kingdom
European Research Council338895
European Union283570
Diamond Light SourceMX-8987 and MX-12788 United Kingdom
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 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)30,3153
Polymers30,1731
Non-polymers1422
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA analysis supports monomeric structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-5 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.210, 39.030, 63.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 6x His-tag at C-terminus / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69052
#2: Chemical ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO3P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: rods
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MMT buffer pH 5 25% (w/v) and 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: 1.52→33.25 Å / Num. obs: 44234 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rpim(I) all: 0.039 / Net I/σ(I): 11.9
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2169 / CC1/2: 0.51 / Rpim(I) all: 0.607 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→33.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.252 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18847 2196 5 %RANDOM
Rwork0.15921 ---
obs0.16064 42000 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.31 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.52→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 8 193 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192042
X-RAY DIFFRACTIONr_bond_other_d0.0010.021910
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9772767
X-RAY DIFFRACTIONr_angle_other_deg0.99834434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14124.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03115343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0121511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
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_it3.3591.7651035
X-RAY DIFFRACTIONr_mcbond_other3.3491.7631034
X-RAY DIFFRACTIONr_mcangle_it4.0052.6211292
X-RAY DIFFRACTIONr_mcangle_other4.0042.6231293
X-RAY DIFFRACTIONr_scbond_it19.1152.3891007
X-RAY DIFFRACTIONr_scbond_other19.1152.3891007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.283.2461476
X-RAY DIFFRACTIONr_long_range_B_refined14.33222.4492142
X-RAY DIFFRACTIONr_long_range_B_other14.3322.4572143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 159 -
Rwork0.28 3064 -
obs--99.97 %

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