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- PDB-5me4: The structure of HtxB from Pseudomonas stutzeri in complex with h... -

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Basic information

Entry
Database: PDB / ID: 5me4
TitleThe structure of HtxB from Pseudomonas stutzeri in complex with hypophosphite to 1.52 A resolution
ComponentsProbable phosphite transport system-binding protein HtxB
KeywordsTRANSPORT PROTEIN / ABC-transporter / periplamic binding protein / phosphite / hypophosphite
Function / homologyPhosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / phosphinate / Probable phosphite transport system-binding protein HtxB
Function and homology information
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBisson, C. / Hitchcock, A.
Funding support United Kingdom, 3items
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 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
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Probable phosphite transport system-binding protein HtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4653
Polymers30,3351
Non-polymers1302
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint6 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.240, 55.210, 125.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30334.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This construct has had an N-terminal signal peptide/anchor removed and a C-terminal 6xHis tag added.
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: htxB / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69061
#2: Chemical ChemComp-HP4 / phosphinate / Hypophosphite


Mass: 64.988 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium/potassium tartrate, 0.1 M Bis-tris propane pH 8.5 and 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.52→22.81 Å / Num. obs: 42787 / % possible obs: 97.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6 % / Rmerge(I) obs: 1.209 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.525 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVB

5jvb


Resolution: 1.52→22.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.532 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19771 2115 4.9 %RANDOM
Rwork0.16732 ---
obs0.1688 40628 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.139 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.52→22.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 6 175 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192093
X-RAY DIFFRACTIONr_bond_other_d0.0020.022051
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9662833
X-RAY DIFFRACTIONr_angle_other_deg0.92334694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99524.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7391510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
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_it4.2771.791044
X-RAY DIFFRACTIONr_mcbond_other4.0751.7841043
X-RAY DIFFRACTIONr_mcangle_it4.7252.6541307
X-RAY DIFFRACTIONr_mcangle_other4.7242.6571308
X-RAY DIFFRACTIONr_scbond_it20.3962.4051049
X-RAY DIFFRACTIONr_scbond_other20.392.4081050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.4643.2541523
X-RAY DIFFRACTIONr_long_range_B_refined15.03522.3132443
X-RAY DIFFRACTIONr_long_range_B_other15.10822.0492412
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
Rfree0.306 167 -
Rwork0.292 2771 -
obs--92.86 %

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