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- PDB-7nsw: The structure of the SBP TarP_Csal in complex with coumarate -

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Basic information

Entry
Database: PDB / ID: 7nsw
TitleThe structure of the SBP TarP_Csal in complex with coumarate
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP transporter / solute binding protein / periplasmic / hydroxycinnamate / lignin
Function / homologyTRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / transmembrane transport / metal ion binding / 4'-HYDROXYCINNAMIC ACID / TRAP dicarboxylate transporter-DctP subunit
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 8, 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 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: TRAP dicarboxylate transporter-DctP subunit
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0718
Polymers74,6082
Non-polymers4636
Water4,252236
1
AAA: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5795
Polymers37,3041
Non-polymers2754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4923
Polymers37,3041
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.170, 119.940, 62.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit


Mass: 37303.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal 6xHis tag and linker region.
Source: (gene. exp.) Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (bacteria)
Strain: ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11
Gene: Csal_0280 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1R0W5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M MgCl2, 0.1 M Hepes pH 7.0 and 25 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.67→34.25 Å / Num. obs: 71530 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Net I/σ(I): 9.8
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5218 / Rpim(I) all: 0.56 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NRR

7nrr


Resolution: 1.67→34.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.778 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2512 3434 4.804 %
Rwork0.1973 68054 -
all0.2 --
obs-71488 99.48 %
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: 25.282 Å2
Baniso -1Baniso -2Baniso -3
1-3.303 Å2-0 Å2-0 Å2
2---1.933 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.67→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5101 0 31 236 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174845
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6477120
X-RAY DIFFRACTIONr_angle_other_deg1.4561.57211171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47622.388289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92215850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3241536
X-RAY DIFFRACTIONr_chiral_restr0.0820.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021163
X-RAY DIFFRACTIONr_nbd_refined0.2070.21049
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.24445
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2213
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.224
X-RAY DIFFRACTIONr_nbd_other0.2130.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.217
X-RAY DIFFRACTIONr_mcbond_it7.9962.2882618
X-RAY DIFFRACTIONr_mcbond_other7.9852.2872617
X-RAY DIFFRACTIONr_mcangle_it7.7313.3793269
X-RAY DIFFRACTIONr_mcangle_other7.7323.383270
X-RAY DIFFRACTIONr_scbond_it21.7892.9872624
X-RAY DIFFRACTIONr_scbond_other21.7852.9862625
X-RAY DIFFRACTIONr_scangle_it18.2884.053851
X-RAY DIFFRACTIONr_scangle_other18.2864.053852
X-RAY DIFFRACTIONr_lrange_it16.13727.5785763
X-RAY DIFFRACTIONr_lrange_other16.13627.5765764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.4141930.3955012X-RAY DIFFRACTION99.2185
1.713-1.760.3682340.3774802X-RAY DIFFRACTION99.2315
1.76-1.8110.362590.3294690X-RAY DIFFRACTION99.3376
1.811-1.8670.3142420.2864601X-RAY DIFFRACTION99.4864
1.867-1.9280.3022080.2444441X-RAY DIFFRACTION99.3801
1.928-1.9960.312270.2254320X-RAY DIFFRACTION99.6057
1.996-2.0710.2812120.2054148X-RAY DIFFRACTION99.4072
2.071-2.1560.252000.1864007X-RAY DIFFRACTION99.6211
2.156-2.2510.2362090.1693835X-RAY DIFFRACTION99.6796
2.251-2.3610.2762040.1763683X-RAY DIFFRACTION99.5391
2.361-2.4890.2641950.1823504X-RAY DIFFRACTION99.7304
2.489-2.6390.2531820.1793319X-RAY DIFFRACTION99.772
2.639-2.8210.2391440.1713164X-RAY DIFFRACTION99.7888
2.821-3.0470.2061500.1722927X-RAY DIFFRACTION99.6761
3.047-3.3370.2421410.1872708X-RAY DIFFRACTION99.6851
3.337-3.730.2311140.1862485X-RAY DIFFRACTION99.5785
3.73-4.3050.2321140.1572170X-RAY DIFFRACTION99.1319
4.305-5.2670.173960.1381868X-RAY DIFFRACTION99.242
5.267-7.4260.203730.1681495X-RAY DIFFRACTION99.809

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