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- PDB-7nte: The structure of an open conformation of the SBP TarP_Csal -

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Basic information

Entry
Database: PDB / ID: 7nte
TitleThe structure of an open conformation of the SBP TarP_Csal
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 / TRAP dicarboxylate transporter-DctP subunit
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter-DctP subunit
B: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6815
Polymers74,6082
Non-polymers733
Water4,936274
1
A: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3282
Polymers37,3041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3523
Polymers37,3041
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.770, 63.620, 73.700
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number4
Space group name H-MP1211

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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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.9 %
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: 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: 1.6→53.43 Å / Num. obs: 74222 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.038 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.603 / Num. unique obs: 5395 / CC1/2: 0.717 / Rpim(I) all: 0.379 / Rrim(I) all: 0.715 / % possible all: 96.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NTD

7ntd


Resolution: 1.6→53.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.91 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 3658 4.9 %RANDOM
Rwork0.1758 ---
obs0.1778 70544 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 22.754 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å2-0.27 Å2
2---1.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.6→53.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 3 274 5365
Biso mean--23.36 27.05 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195202
X-RAY DIFFRACTIONr_bond_other_d0.0020.024741
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9617071
X-RAY DIFFRACTIONr_angle_other_deg0.96310995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.824.217249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38415846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6461536
X-RAY DIFFRACTIONr_chiral_restr0.0810.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021036
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 246 -
Rwork0.244 5140 -
all-5386 -
obs--96.52 %

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