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- PDB-5lq1: 1.41 A resolution structure of PtxB from Trichodesmium erythraeum... -

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Basic information

Entry
Database: PDB / ID: 5lq1
Title1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate
ComponentsPhosphonate ABC transporter, periplasmic phosphonate-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / phosphite / methylphosphonate / periplasmic binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / metal ion binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYLPHOSPHONIC ACID ESTER GROUP / Phosphonate ABC transporter, periplasmic phosphonate-binding protein
Similarity search - Component
Biological speciesTrichodesmium erythraeum IMS101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
B: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6989
Polymers62,3472
Non-polymers3517
Water3,837213
1
A: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3805
Polymers31,1731
Non-polymers2074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3184
Polymers31,1731
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.481, 53.703, 66.388
Angle α, β, γ (deg.)84.82, 78.26, 69.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphonate ABC transporter, periplasmic phosphonate-binding protein


Mass: 31173.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct is truncated by 26 residues at the N-termius to remove a signal peptide.
Source: (gene. exp.) Trichodesmium erythraeum IMS101 (bacteria)
Gene: Tery_0366 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q119I9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GB / METHYLPHOSPHONIC ACID ESTER GROUP


Mass: 96.022 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5O3P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Magnesium chloride, 0.1 M Sodium acetate pH 5.0 and 20 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.41→65.05 Å / Num. obs: 91920 / % possible obs: 95.2 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 9.1
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.48 / % possible all: 75.4

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Processing

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

5jvb


Resolution: 1.41→64.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.251 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23031 4350 4.8 %RANDOM
Rwork0.1798 ---
obs0.18221 86075 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.69 Å2-0.29 Å2
2--0.15 Å2-0.18 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.41→64.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 18 213 4229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024092
X-RAY DIFFRACTIONr_bond_other_d0.0030.024025
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9835532
X-RAY DIFFRACTIONr_angle_other_deg1.10939313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50626.534176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9815757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.193158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214591
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02833
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_it3.8911.8872062
X-RAY DIFFRACTIONr_mcbond_other3.8911.8842061
X-RAY DIFFRACTIONr_mcangle_it4.0882.812574
X-RAY DIFFRACTIONr_mcangle_other4.0892.8122575
X-RAY DIFFRACTIONr_scbond_it9.5442.6232030
X-RAY DIFFRACTIONr_scbond_other9.5442.6232030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0963.5372959
X-RAY DIFFRACTIONr_long_range_B_refined6.45824.3314642
X-RAY DIFFRACTIONr_long_range_B_other6.45824.3334643
X-RAY DIFFRACTIONr_rigid_bond_restr8.72338117
X-RAY DIFFRACTIONr_sphericity_free20.522573
X-RAY DIFFRACTIONr_sphericity_bonded31.37358199
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 239 -
Rwork0.407 5190 -
obs--76.27 %

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