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- PDB-7nra: The structure of the SBP TarP_Sse in complex with cinnamate -

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Basic information

Entry
Database: PDB / ID: 7nra
TitleThe structure of the SBP TarP_Sse in complex with cinnamate
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / solute binding protein / TRAP transporter / lignin / hydroxycinnamate
Function / homologyTRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / periplasmic space / HYDROCINNAMIC ACID / TRAP dicarboxylate transporter, DctP subunit
Function and homology information
Biological speciesSagittula stellata E-37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBisson, C. / Salmon, R.C. / West, L. / Rafferty, J.B. / Hitchcock, A. / Thomas, G.H. / Kelly, D.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
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 3, 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)74,1814
Polymers73,8812
Non-polymers3002
Water4,990277
1
AAA: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0902
Polymers36,9401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0902
Polymers36,9401
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.120, 70.200, 85.010
Angle α, β, γ (deg.)90.000, 93.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36940.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal linker and 6xHis tag. / Source: (gene. exp.) Sagittula stellata E-37 (bacteria) / Gene: SSE37_24379 / Production host: Escherichia coli (E. coli) / References: UniProt: A3K0X1
#2: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.59 Å3/Da / Density % sol: 52.43 % / Description: large cuboidal
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.91→64.02 Å / Num. obs: 57762 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.079 / Net I/σ(I): 9.9
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4328 / Rpim(I) all: 0.41 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NR2

7nr2


Resolution: 1.91→64.02 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.108 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2608 2852 4.939 %
Rwork0.2001 54893 -
all0.203 --
obs-57745 98.499 %
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: 30.818 Å2
Baniso -1Baniso -2Baniso -3
1--1.606 Å20 Å20.697 Å2
2---1.28 Å20 Å2
3---2.793 Å2
Refinement stepCycle: LAST / Resolution: 1.91→64.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5015 0 22 277 5314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135155
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174664
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6437028
X-RAY DIFFRACTIONr_angle_other_deg1.3151.57610859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38724.538249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29315810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9951518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215847
X-RAY DIFFRACTIONr_gen_planes_other0.0110.0221003
X-RAY DIFFRACTIONr_nbd_refined0.2030.21122
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.24443
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22504
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.28
X-RAY DIFFRACTIONr_nbd_other0.2290.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.210
X-RAY DIFFRACTIONr_mcbond_it26.1863.0472618
X-RAY DIFFRACTIONr_mcbond_other26.0763.0442617
X-RAY DIFFRACTIONr_mcangle_it21.7894.4573269
X-RAY DIFFRACTIONr_mcangle_other21.8184.463270
X-RAY DIFFRACTIONr_scbond_it30.1043.4672537
X-RAY DIFFRACTIONr_scbond_other30.1073.4672536
X-RAY DIFFRACTIONr_scangle_it24.944.913759
X-RAY DIFFRACTIONr_scangle_other24.9414.913759
X-RAY DIFFRACTIONr_lrange_it25.03936.585807
X-RAY DIFFRACTIONr_lrange_other25.03736.5775808
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
1.91-1.960.3312070.2741190.27343350.810.83499.79240.27
1.96-2.0130.2971700.25140060.25341930.8320.86199.59460.251
2.013-2.0720.3281860.23539110.23941090.8230.87899.7080.235
2.072-2.1350.2581750.21237550.21439540.8950.90899.3930.212
2.135-2.2050.2882020.20936420.21338670.8750.90699.40520.209
2.205-2.2820.2682060.19134650.19636920.8930.92399.43120.191
2.282-2.3690.2721850.19433950.19836110.8980.91999.14150.194
2.369-2.4650.2681590.1932590.19334540.9020.92698.95770.19
2.465-2.5750.2731560.20131300.20433240.8970.9298.85680.201
2.575-2.70.2771850.20629570.21131870.8870.91298.5880.206
2.7-2.8460.2991430.20628000.2129870.8810.92398.52690.206
2.846-3.0180.2781330.23326810.23528850.8830.8997.5390.233
3.018-3.2260.3181200.23625080.2426890.8740.88797.73150.236
3.226-3.4840.2971160.21723480.22125150.8790.90697.97220.217
3.484-3.8150.2421030.18721310.18923280.9190.93795.96220.187
3.815-4.2630.2091030.15919340.16121010.9460.95696.95380.159
4.263-4.9190.2171000.13916670.14318520.9590.96995.41040.139
4.919-6.0160.225750.17214620.17515870.9380.95496.84940.172
6.016-8.4710.204730.17711210.17912360.9470.94696.60190.177
8.471-64.0250.169550.2026010.1997170.9640.9591.49230.202

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