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- PDB-7nqg: The structure of the SBP TarP_Rhp in complex with 4-hydroxyphenyl... -

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Basic information

Entry
Database: PDB / ID: 7nqg
TitleThe structure of the SBP TarP_Rhp in complex with 4-hydroxyphenylacetate
ComponentsTrapT family, dctP subunit, C4-dicarboxylate periplasmic binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / TRAP transporter / solute binding protein / hydroxycinnamate
Function / homologyTRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / 4-HYDROXYPHENYLACETATE / PHOSPHATE ION / TRAP transporter substrate-binding protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsBisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)
CitationJournal: Febs J. / Year: 2022
Title: The structural basis for high-affinity uptake of lignin-derived aromatic compounds by proteobacterial TRAP transporters.
Authors: Bisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 23, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: TrapT family, dctP subunit, C4-dicarboxylate periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8225
Polymers36,4501
Non-polymers3714
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint7 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 50.500, 142.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TrapT family, dctP subunit, C4-dicarboxylate periplasmic binding protein


Mass: 36450.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M1-D4 sequence not visible in structure. N-terminal residue was found to be a PCA, formed by spontaneous cyclisation on an N-terminal glutamine (Q5). 6xHis tag on C-terminus.
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1782 / Plasmid: pET22b+ (pelB) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N8X0
#2: Chemical ChemComp-4HP / 4-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.84 % / Description: Plates
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl pH 8 and 20 % (w/v) PEG 6000 (+6 mM coumarate - not bound)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 29, 2014
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.1→50.5 Å / Num. obs: 113835 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Net I/σ(I): 17
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7978 / Rpim(I) all: 0.328 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→47.647 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.767 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1384 5623 4.944 %
Rwork0.1178 108113 -
all0.119 --
obs-113736 99.583 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.026 Å20 Å2-0 Å2
2---0.128 Å20 Å2
3---0.102 Å2
Refinement stepCycle: LAST / Resolution: 1.1→47.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 24 373 2880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132647
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172486
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.6473609
X-RAY DIFFRACTIONr_angle_other_deg1.5931.5885775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53923.471121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16415441
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.546153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.939159
X-RAY DIFFRACTIONr_chiral_restr0.1110.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02582
X-RAY DIFFRACTIONr_nbd_refined0.2210.2553
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22224
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21253
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2207
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.218
X-RAY DIFFRACTIONr_nbd_other0.1850.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_mcbond_it1.0570.9221296
X-RAY DIFFRACTIONr_mcbond_other1.0540.9211295
X-RAY DIFFRACTIONr_mcangle_it1.4161.3961625
X-RAY DIFFRACTIONr_mcangle_other1.4151.3971626
X-RAY DIFFRACTIONr_scbond_it1.7311.1511351
X-RAY DIFFRACTIONr_scbond_other1.731.1491348
X-RAY DIFFRACTIONr_scangle_it2.0811.6221975
X-RAY DIFFRACTIONr_scangle_other2.0771.6181970
X-RAY DIFFRACTIONr_lrange_it2.90112.2983091
X-RAY DIFFRACTIONr_lrange_other2.90112.3023092
X-RAY DIFFRACTIONr_rigid_bond_restr2.51635133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.1290.2344050.2237569X-RAY DIFFRACTION95.8183
1.129-1.1590.1943880.1777631X-RAY DIFFRACTION99.0122
1.159-1.1930.1593900.1497540X-RAY DIFFRACTION99.8866
1.193-1.230.153860.1257350X-RAY DIFFRACTION99.8967
1.23-1.270.1413780.1137050X-RAY DIFFRACTION99.9731
1.27-1.3150.143310.1096873X-RAY DIFFRACTION99.9168
1.315-1.3640.123630.0996635X-RAY DIFFRACTION100
1.364-1.420.1243150.0916416X-RAY DIFFRACTION99.9406
1.42-1.4830.1193060.0886159X-RAY DIFFRACTION99.9073
1.483-1.5550.123010.0845876X-RAY DIFFRACTION99.9515
1.555-1.6390.1153230.0835567X-RAY DIFFRACTION100
1.639-1.7390.1062980.0855294X-RAY DIFFRACTION99.9821
1.739-1.8590.1232670.0914990X-RAY DIFFRACTION100
1.859-2.0070.1132230.0974696X-RAY DIFFRACTION99.9797
2.007-2.1980.1152270.1064334X-RAY DIFFRACTION99.9781
2.198-2.4570.1471920.1123922X-RAY DIFFRACTION99.9514
2.457-2.8360.1531730.1253483X-RAY DIFFRACTION100
2.836-3.4710.1481450.1362996X-RAY DIFFRACTION100
3.471-4.8970.1471300.1342360X-RAY DIFFRACTION99.9197

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