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- PDB-7nr2: The structure of the SBP TarP_Sse in complex with coumarate -

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Basic information

Entry
Database: PDB / ID: 7nr2
TitleThe structure of the SBP TarP_Sse in complex with coumarate
ComponentsTRAP dicarboxylate transporter, DctP subunit
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 / periplasmic space / 4'-HYDROXYCINNAMIC ACID / TRAP dicarboxylate transporter, DctP subunit
Function and homology information
Biological speciesSagittula stellata E-37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.13 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 2, 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

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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
CCC: TRAP dicarboxylate transporter, DctP subunit
EEE: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,69316
Polymers150,2004
Non-polymers1,49312
Water7,656425
1
AAA: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8103
Polymers37,5501
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1947
Polymers37,5501
Non-polymers6446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8783
Polymers37,5501
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
EEE: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8103
Polymers37,5501
Non-polymers2602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.840, 88.080, 96.580
Angle α, β, γ (deg.)90.000, 92.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRAP dicarboxylate transporter, DctP subunit


Mass: 37549.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SeMet derivative. C-terminal linker and 6xHIS tag, not visible in structure.
Source: (gene. exp.) Sagittula stellata E-37 (bacteria) / Gene: SSE37_24379 / Production host: Escherichia coli (E. coli) / References: UniProt: A3K0X1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 0.2 M NaCl, 0.1 M sodium cacodylate pH 6.25 and 1.8 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97918, 0.97938
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979381
ReflectionResolution: 2.13→50.5 Å / Num. obs: 77509 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.062 / Net I/σ(I): 12.5
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5746 / Rpim(I) all: 0.343 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSxia2data reduction
XSCALExia2data scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.13→50.496 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.078 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2363 3698 4.772 %
Rwork0.1796 73792 -
all0.182 --
obs-77490 99.698 %
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: 35.713 Å2
Baniso -1Baniso -2Baniso -3
1--1.468 Å2-0 Å2-0.059 Å2
2--0.895 Å20 Å2
3---0.577 Å2
Refinement stepCycle: LAST / Resolution: 2.13→50.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9904 0 95 425 10424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179386
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.64713977
X-RAY DIFFRACTIONr_angle_other_deg1.3011.57521719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33951289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29724.371501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.478151460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9731536
X-RAY DIFFRACTIONr_chiral_restr0.0820.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022150
X-RAY DIFFRACTIONr_nbd_refined0.2130.22257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.28891
X-RAY DIFFRACTIONr_nbtor_refined0.170.24864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2430
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.210
X-RAY DIFFRACTIONr_nbd_other0.1930.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.28
X-RAY DIFFRACTIONr_mcbond_it3.2683.5885159
X-RAY DIFFRACTIONr_mcbond_other3.2683.5885158
X-RAY DIFFRACTIONr_mcangle_it4.5155.3676444
X-RAY DIFFRACTIONr_mcangle_other4.5145.3686445
X-RAY DIFFRACTIONr_scbond_it4.1163.935085
X-RAY DIFFRACTIONr_scbond_other4.1043.9275082
X-RAY DIFFRACTIONr_scangle_it6.0155.7327532
X-RAY DIFFRACTIONr_scangle_other5.9965.7277527
X-RAY DIFFRACTIONr_lrange_it7.21542.71611267
X-RAY DIFFRACTIONr_lrange_other7.21542.71411268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.13-2.1850.3162860.26954480.27157450.8180.83699.80850.251
2.185-2.2450.2842650.25152990.25355750.8610.86599.80270.229
2.245-2.310.2922650.23351360.23654110.8710.89199.81520.209
2.31-2.3810.2892510.22950060.23252590.8640.88599.9620.205
2.381-2.4590.3062280.21948530.22350870.8770.89899.88210.195
2.459-2.5450.2881980.21547350.21849380.8840.90699.89870.191
2.545-2.6410.2992080.19645300.247440.9010.92499.87350.174
2.641-2.7480.2622270.19943960.20246290.9070.92199.87040.178
2.748-2.870.2752670.2141010.21443750.8970.91199.840.191
2.87-3.010.2741700.20140400.20442150.8950.92799.88140.184
3.01-3.1720.2861950.20138190.20540180.9010.9399.90050.19
3.172-3.3630.2461900.19935960.20137960.9180.93699.73660.191
3.363-3.5940.2141800.16933700.17135730.9420.9699.35630.165
3.594-3.8810.21980.15130870.15433050.9550.96599.39490.15
3.881-4.2490.1861100.14629570.14730890.9570.96399.28780.148
4.249-4.7460.1521220.12126340.12227790.9750.97999.17240.123
4.746-5.4720.1651200.12923540.13124880.970.97999.43730.132
5.472-6.6820.215820.15919860.16120790.9480.96399.47090.16
6.682-9.3690.184910.14815590.1516590.960.96899.45750.156
9.369-50.4960.274450.1528850.1569530.9170.97597.58660.166

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