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- PDB-5lq5: 1.46 A resolution structure of PhnD1 from Prochlorococcus marinus... -

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Basic information

Entry
Database: PDB / ID: 5lq5
Title1.46 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with phosphite
ComponentsPutative phosphonate binding protein for ABC transporter
KeywordsTRANSPORT PROTEIN / ABC-transporter / phosphite / Prochlorococcus / periplasmic binding protein
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 / PHOSPHITE ION / 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: 1.46 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/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)32,4082
Polymers32,3291
Non-polymers791
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint1 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.330, 57.610, 54.790
Angle α, β, γ (deg.)90.00, 107.15, 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 has been truncated by 24 residues on 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-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) 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: 1.46→44.27 Å / Num. obs: 46137 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Net I/σ(I): 15.8
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.569 / % possible all: 78.4

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Processing

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

5jvb


Resolution: 1.46→44.27 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.675 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2244 4.8 %RANDOM
Rwork0.14597 ---
obs0.14764 44161 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-1.47 Å2
2--1.46 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.46→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 4 129 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192271
X-RAY DIFFRACTIONr_bond_other_d0.0030.022257
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9533056
X-RAY DIFFRACTIONr_angle_other_deg1.33835191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93824.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83715437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9471512
X-RAY DIFFRACTIONr_chiral_restr0.1690.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022563
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02537
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_it4.4332.5341101
X-RAY DIFFRACTIONr_mcbond_other3.6792.531100
X-RAY DIFFRACTIONr_mcangle_it4.2293.7911375
X-RAY DIFFRACTIONr_mcangle_other4.3733.7961376
X-RAY DIFFRACTIONr_scbond_it11.5193.5371170
X-RAY DIFFRACTIONr_scbond_other11.5293.5431168
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.9234.7981677
X-RAY DIFFRACTIONr_long_range_B_refined7.71632.12635
X-RAY DIFFRACTIONr_long_range_B_other7.75831.7822588
X-RAY DIFFRACTIONr_rigid_bond_restr9.1834528
X-RAY DIFFRACTIONr_sphericity_free22.292540
X-RAY DIFFRACTIONr_sphericity_bonded30.61154575
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 139 -
Rwork0.298 2668 -
obs--79.03 %

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