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- PDB-7nrr: The structure of the SBP TarP_Csal in complex with caffeate -

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Basic information

Entry
Database: PDB / ID: 7nrr
TitleThe structure of the SBP TarP_Csal in complex with caffeate
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / transmembrane transport / metal ion binding / CAFFEIC ACID / TRAP dicarboxylate transporter-DctP subunit
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.67 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 4, 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 1.2Nov 6, 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: TRAP dicarboxylate transporter-DctP subunit
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8107
Polymers75,3772
Non-polymers4335
Water4,414245
1
AAA: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8933
Polymers37,6881
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9174
Polymers37,6881
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.730, 119.540, 61.940
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: 37688.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein was expressed in the presence of seleno-methionine. C-terminal linker and 6xHis tag.
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M MgCl2, 0.1 M MES pH 6.0 and 20% (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 / Wavelength: 0.97258, 0.97841, 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.972581
20.978411
30.976251
ReflectionResolution: 1.67→67.47 Å / Num. obs: 70139 / % possible obs: 98.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.029 / Net I/σ(I): 18.4
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2 / Num. unique obs: 4567 / Rpim(I) all: 0.346 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.67→67.468 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.944 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2652 3439 4.907 %
Rwork0.2056 66643 -
all0.209 --
obs-70082 98.511 %
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: 23.702 Å2
Baniso -1Baniso -2Baniso -3
1-4.156 Å20 Å20 Å2
2---2.504 Å20 Å2
3----1.653 Å2
Refinement stepCycle: LAST / Resolution: 1.67→67.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 29 245 5376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174760
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6547125
X-RAY DIFFRACTIONr_angle_other_deg1.3321.56811038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00822.353289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6191536
X-RAY DIFFRACTIONr_chiral_restr0.0710.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021085
X-RAY DIFFRACTIONr_nbd_refined0.1940.21174
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24611
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.216
X-RAY DIFFRACTIONr_nbd_other0.1880.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.227
X-RAY DIFFRACTIONr_mcbond_it7.7622.1042618
X-RAY DIFFRACTIONr_mcbond_other7.7262.1032617
X-RAY DIFFRACTIONr_mcangle_it7.8773.1123269
X-RAY DIFFRACTIONr_mcangle_other7.883.1133270
X-RAY DIFFRACTIONr_scbond_it26.7222.8252625
X-RAY DIFFRACTIONr_scbond_other26.7172.8242626
X-RAY DIFFRACTIONr_scangle_it20.8583.8093856
X-RAY DIFFRACTIONr_scangle_other20.8563.8083857
X-RAY DIFFRACTIONr_lrange_it18.85626.4435913
X-RAY DIFFRACTIONr_lrange_other18.88926.3975888
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
1.67-1.7130.4152270.38243380.38451860.510.60288.02550.382
1.713-1.760.3782380.36445940.36550670.3580.41195.36210.364
1.76-1.8110.3742500.3246390.32249510.6010.63598.74770.32
1.811-1.8670.3222400.28944990.2947570.7520.75999.62160.289
1.867-1.9280.3112090.2544330.25246580.8060.84499.65650.25
1.928-1.9960.2912230.22142650.22444980.860.89399.77770.221
1.996-2.0710.2772130.20341260.20743530.8770.91399.67840.203
2.071-2.1560.2261960.17539690.17741730.920.93799.80830.175
2.156-2.2510.2652150.18937950.19340220.90.92799.70160.189
2.251-2.3610.271930.1736490.17538490.9110.9499.81810.17
2.361-2.4890.2711960.18634710.19136750.9120.93199.78230.186
2.489-2.6390.2741800.18932970.19334860.9170.93499.74180.189
2.639-2.8210.2651400.18831310.19132760.9030.93699.84740.188
2.821-3.0470.2341520.19628870.19830450.9230.93499.8030.196
3.047-3.3370.2551440.21126810.21328320.920.92899.75280.211
3.337-3.730.2641080.20324780.20625930.9260.94199.730.203
3.73-4.3050.2261120.16121670.16422820.9410.96499.86850.161
4.305-5.2670.197950.14518590.14719600.9650.97399.69390.145
5.267-7.4250.218710.16614810.16915530.9660.96499.93560.166
7.425-67.4680.191370.1918840.1919250.9480.95999.56760.191

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