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- PDB-5lq8: 1.52 A resolution structure of PhnD1 from Prochlorococcus marinus... -

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Basic information

Entry
Database: PDB / ID: 5lq8
Title1.52 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with methylphosphonate
ComponentsPutative phosphonate binding protein for ABC transporter
KeywordsPERIPLASMIC BINDING PROTEIN / ABC-transporter / methylphosphonate / Prochlorococcus
Function / homologyPutative ABC transporter periplasmic binding protein PhnD-like / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / METHYLPHOSPHONIC ACID ESTER GROUP / Probable ABC transporter phosphite binding protein PhnD1
Function and homology information
Biological speciesProchlorococcus marinus str. MIT 9301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBisson, C. / Adams, N.B.P. / Polyviou, D. / Bibby, T.S. / Hunter, C.N. / Hitchcock, A.
Funding support United Kingdom, 4items
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
NERC and A. G. Leventis Foundation PhD studentship 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
DepositionAug 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Putative phosphonate binding protein for ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5213
Polymers32,3291
Non-polymers1922
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint5 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.860, 57.080, 54.170
Angle α, β, γ (deg.)90.00, 106.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative phosphonate binding protein for ABC transporter


Mass: 32329.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct is truncated by 24 residues at the N-terminus to remove a signal peptide and has a C-terminal 6XHis tag.
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9301 (bacteria)
Gene: phnD, P9301_07261 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3PC74
#2: Chemical ChemComp-GB / METHYLPHOSPHONIC ACID ESTER GROUP


Mass: 96.022 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M MMT (DL-malic acid, MES and Tris base) buffer pH 8.0 and 25% (w/v) PEG 1500

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.52→44 Å / Num. obs: 40089 / % possible obs: 97 % / Redundancy: 2.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.021 / Net I/σ(I): 16.2
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.679 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LQ5

5lq5


Resolution: 1.52→44 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.481 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20707 1919 4.8 %RANDOM
Rwork0.15759 ---
obs0.15997 38156 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-2.46 Å2
2--1.29 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.52→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 10 91 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192241
X-RAY DIFFRACTIONr_bond_other_d0.0030.022223
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9563016
X-RAY DIFFRACTIONr_angle_other_deg1.32235111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69625.234107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8091510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022521
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02525
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_it7.5772.9531087
X-RAY DIFFRACTIONr_mcbond_other7.5372.9521086
X-RAY DIFFRACTIONr_mcangle_it7.9464.3951357
X-RAY DIFFRACTIONr_mcangle_other7.9744.3961358
X-RAY DIFFRACTIONr_scbond_it11.2943.7881154
X-RAY DIFFRACTIONr_scbond_other11.3023.791152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.5525.2551660
X-RAY DIFFRACTIONr_long_range_B_refined8.88335.8442536
X-RAY DIFFRACTIONr_long_range_B_other8.91235.6632505
X-RAY DIFFRACTIONr_rigid_bond_restr10.18434464
X-RAY DIFFRACTIONr_sphericity_free20.86529
X-RAY DIFFRACTIONr_sphericity_bonded31.7854487
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 121 -
Rwork0.306 2654 -
obs--92.19 %

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