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- PDB-8trp: Structure of a HEPES bound TRAP transporter substrate binding protein. -

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Basic information

Entry
Database: PDB / ID: 8trp
TitleStructure of a HEPES bound TRAP transporter substrate binding protein.
ComponentsIsethionate-binding periplasmic protein DctP
KeywordsTRANSPORT PROTEIN / TRAP Transporter / substrate binding protein
Function / homologyalkanesulfonate catabolic process / TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / Isethionate-binding periplasmic protein DctP
Function and homology information
Biological speciesOleidesulfovibrio alaskensis G20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsNewton-Vesty, M.C. / Dobson, R.C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: Biochem.J. / Year: 2024
Title: On the function of TRAP substrate-binding proteins: the isethionate-specific binding protein IseP.
Authors: Newton-Vesty, M.C. / Currie, M.J. / Davies, J.S. / Panjikar, S. / Sethi, A. / Whitten, A.E. / Tillett, Z.D. / Wood, D.M. / Wright, J.D. / Love, M.J. / Allison, T.M. / Jamieson, S.A. / Mace, ...Authors: Newton-Vesty, M.C. / Currie, M.J. / Davies, J.S. / Panjikar, S. / Sethi, A. / Whitten, A.E. / Tillett, Z.D. / Wood, D.M. / Wright, J.D. / Love, M.J. / Allison, T.M. / Jamieson, S.A. / Mace, P.D. / North, R.A. / Dobson, R.C.J.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isethionate-binding periplasmic protein DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6504
Polymers37,2881
Non-polymers3623
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.588, 73.208, 94.818
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isethionate-binding periplasmic protein DctP / TRAP transporter / DctP solute-binding subunit


Mass: 37287.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleidesulfovibrio alaskensis G20 (bacteria)
Gene: dctP, Dde_1275 / Production host: Escherichia coli (E. coli) / References: UniProt: Q312S0
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 20% PEG 4000, 10% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.89→47.454 Å / Num. obs: 26163 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.016 / Rrim(I) all: 0.06 / Net I/σ(I): 35.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.06-47.4120.40.0392940.9990.0110.041
1.89-1.93260.47116470.9820.1320.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOLREPphasing
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→47.454 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.183 / SU B: 3.208 / SU ML: 0.095 / Average fsc free: 0.9617 / Average fsc work: 0.9779 / Cross valid method: NONE / ESU R: 0.144 / ESU R Free: 0.143 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2294 1371 5.251 %
Rwork0.1747 24738 -
all0.178 --
obs-26109 99.973 %
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: 34.663 Å2
Baniso -1Baniso -2Baniso -3
1-2.847 Å2-0 Å20 Å2
2---1.93 Å2-0 Å2
3----0.917 Å2
Refinement stepCycle: LAST / Resolution: 1.89→47.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 23 179 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122479
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.8413363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.444511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10310435
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93610109
X-RAY DIFFRACTIONr_chiral_restr0.1250.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021862
X-RAY DIFFRACTIONr_nbd_refined0.2140.21139
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2170
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.210
X-RAY DIFFRACTIONr_mcbond_it3.0293.1211242
X-RAY DIFFRACTIONr_mcangle_it3.7825.5891554
X-RAY DIFFRACTIONr_scbond_it4.823.5961237
X-RAY DIFFRACTIONr_scangle_it7.0336.3681806
X-RAY DIFFRACTIONr_lrange_it7.70136.6673852
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
1.89-1.9390.244930.20117850.20318840.9590.97499.68150.178
1.939-1.9920.331160.19517350.20318510.9390.9751000.175
1.992-2.050.244750.19117210.19417960.9580.9771000.175
2.05-2.1130.2931010.216380.20517390.9490.9741000.183
2.113-2.1820.251030.19416170.19717200.9620.9781000.181
2.182-2.2580.278890.19815480.20216370.9480.9761000.184
2.258-2.3430.271680.19415220.19815900.9520.9761000.183
2.343-2.4390.256800.20814540.2115340.9620.9731000.195
2.439-2.5470.251680.19214120.19514800.9650.9771000.182
2.547-2.6710.233630.19913470.20114100.9610.9761000.194
2.671-2.8150.28650.19912740.20313390.9670.9761000.196
2.815-2.9850.275790.19212020.19712810.960.9761000.194
2.985-3.190.215700.18911370.19112070.9710.9781000.196
3.19-3.4440.225450.17310830.17511280.9740.9821000.183
3.444-3.7710.188590.1559940.15710530.9790.9861000.169
3.771-4.2130.167580.1528820.1539400.9840.9871000.171
4.213-4.8580.212460.1288080.1318540.9790.9911000.149
4.858-5.9350.199380.1576860.167240.9750.9851000.182
5.935-8.3280.232360.1795490.1825850.9830.9851000.204
8.328-47.4540.212190.1483440.1513630.9830.9871000.194

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