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- PDB-7ntd: The structure of the SBP TarP_Csal in complex with ferulate -

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Basic information

Entry
Database: PDB / ID: 7ntd
TitleThe structure of the SBP TarP_Csal in complex with ferulate
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 / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / TRAP dicarboxylate transporter-DctP subunit
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 9, 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

Downloads & links

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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)75,1417
Polymers74,6082
Non-polymers5335
Water8,503472
1
AAA: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6184
Polymers37,3041
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5223
Polymers37,3041
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.860, 52.280, 68.530
Angle α, β, γ (deg.)101.680, 98.590, 104.900
Int Tables number1
Space group name H-MP1

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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
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-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 20 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→48.89 Å / Num. obs: 62516 / % possible obs: 96.8 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.073 / Net I/σ(I): 6.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.687 / Num. unique obs: 4572 / CC1/2: 0.47 / Rpim(I) all: 0.62 / % possible all: 95.4

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Processing

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

7nsw


Resolution: 1.75→47.124 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.876 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2517 3047 4.875 %
Rwork0.1912 59460 -
all0.194 --
obs-62507 96.822 %
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: 33.081 Å2
Baniso -1Baniso -2Baniso -3
1--1.778 Å2-0.73 Å20.443 Å2
2--0.895 Å20.543 Å2
3---0.474 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 35 472 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135152
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174759
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.6467001
X-RAY DIFFRACTIONr_angle_other_deg1.3281.57310970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66522.226283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04515834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3121536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_nbd_refined0.1990.21091
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.24539
X-RAY DIFFRACTIONr_nbtor_refined0.160.22467
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2373
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.29
X-RAY DIFFRACTIONr_nbd_other0.1880.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.218
X-RAY DIFFRACTIONr_mcbond_it15.08532566
X-RAY DIFFRACTIONr_mcbond_other15.0692.9992565
X-RAY DIFFRACTIONr_mcangle_it14.3384.4413204
X-RAY DIFFRACTIONr_mcangle_other14.3364.4423205
X-RAY DIFFRACTIONr_scbond_it32.7073.8722586
X-RAY DIFFRACTIONr_scbond_other32.7063.8652581
X-RAY DIFFRACTIONr_scangle_it24.5445.3223797
X-RAY DIFFRACTIONr_scangle_other24.5045.3063792
X-RAY DIFFRACTIONr_lrange_it23.34137.7085890
X-RAY DIFFRACTIONr_lrange_other23.33937.7065891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3822250.3384340X-RAY DIFFRACTION95.3425
1.795-1.8450.3522400.3114214X-RAY DIFFRACTION95.477
1.845-1.8980.3312220.264071X-RAY DIFFRACTION95.6125
1.898-1.9560.3322260.2324008X-RAY DIFFRACTION96.0526
1.956-2.020.3252040.2373911X-RAY DIFFRACTION96.483
2.02-2.0910.2811860.2073790X-RAY DIFFRACTION96.5986
2.091-2.170.3021520.2053685X-RAY DIFFRACTION96.3102
2.17-2.2580.2811640.1983531X-RAY DIFFRACTION97.0071
2.258-2.3580.2491700.1823385X-RAY DIFFRACTION96.8401
2.358-2.4730.2691810.1793218X-RAY DIFFRACTION97.1698
2.473-2.6070.2591490.1833104X-RAY DIFFRACTION97.3661
2.607-2.7640.2941490.1792932X-RAY DIFFRACTION97.5
2.764-2.9550.2351380.1722747X-RAY DIFFRACTION97.7635
2.955-3.190.2361300.1872546X-RAY DIFFRACTION98.1298
3.19-3.4930.2261130.1942412X-RAY DIFFRACTION98.1345
3.493-3.9030.2221170.1662146X-RAY DIFFRACTION98.3485
3.903-4.5020.197980.1511905X-RAY DIFFRACTION98.67
4.502-5.5020.188810.1591595X-RAY DIFFRACTION98.5303
5.502-7.7330.217610.2021241X-RAY DIFFRACTION97.4551
7.733-47.1240.268410.214679X-RAY DIFFRACTION96.9044

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