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- PDB-8t9t: Apo Crystal Structure of a Substrate Binding Protein (IseP) from ... -

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Basic information

Entry
Database: PDB / ID: 8t9t
TitleApo Crystal Structure of a Substrate Binding Protein (IseP) from an Isethionate TRAP Transporter
ComponentsIsethionate-binding periplasmic protein DctP
KeywordsTRANSPORT PROTEIN / Substrate binding protein / TRAP transporter / Isethionate
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: 1.48 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
DepositionJun 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,6077
Polymers37,2881
Non-polymers3196
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.925, 72.997, 95.24
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Sodium bromide, Bis-Tris propane, PEG 3350

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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: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.48→47.665 Å / Num. obs: 50754 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Net I/σ(I): 25.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.11-47.62160.0643770.9940.0220.068
1.48-1.5120.50.53924530.9750.1740.566

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→47.665 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.248 / SU ML: 0.048 / Cross valid method: NONE / ESU R: 0.073 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.203 2541 5.013 %
Rwork0.17 48143 -
all0.172 --
obs-50684 99.984 %
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 Å2
Baniso -1Baniso -2Baniso -3
1-1.288 Å20 Å20 Å2
2---0.181 Å20 Å2
3----1.107 Å2
Refinement stepCycle: LAST / Resolution: 1.48→47.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 18 393 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122619
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162521
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.853564
X-RAY DIFFRACTIONr_angle_other_deg0.6831.7735839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.687513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44510486
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.24910118
X-RAY DIFFRACTIONr_chiral_restr0.1050.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_nbd_refined0.2550.2631
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22317
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1920.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.221
X-RAY DIFFRACTIONr_nbd_other0.2360.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.226
X-RAY DIFFRACTIONr_mcbond_it1.7052.0011296
X-RAY DIFFRACTIONr_mcbond_other1.70121296
X-RAY DIFFRACTIONr_mcangle_it2.3173.5931637
X-RAY DIFFRACTIONr_mcangle_other2.3293.5951638
X-RAY DIFFRACTIONr_scbond_it3.1642.3621323
X-RAY DIFFRACTIONr_scbond_other3.1642.3631324
X-RAY DIFFRACTIONr_scangle_it4.6084.1731914
X-RAY DIFFRACTIONr_scangle_other4.6074.1741915
X-RAY DIFFRACTIONr_lrange_it5.65125.1693255
X-RAY DIFFRACTIONr_lrange_other5.58222.2983142
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
1.48-1.5180.2292060.20334850.20536910.9660.9711000.182
1.518-1.560.2321860.19634040.19835900.9630.9731000.177
1.56-1.6050.2161490.18133580.18235090.9660.97799.9430.163
1.605-1.6540.2161510.17532680.17734190.9690.9791000.157
1.654-1.7090.2451700.17531180.17932890.9620.9899.96960.16
1.709-1.7690.2111520.17330500.17532020.9720.9811000.159
1.769-1.8350.2231520.16829250.17130770.9680.9821000.156
1.835-1.910.2141690.16928280.17129970.9720.9821000.161
1.91-1.9950.2041540.17326960.17528500.9770.9811000.169
1.995-2.0920.1921530.17225960.17327490.9770.9811000.171
2.092-2.2050.2011100.16425090.16526200.9730.98499.96180.168
2.205-2.3380.1721190.15723550.15824740.9830.9851000.166
2.338-2.4990.1861180.15922400.1623580.9770.9841000.174
2.499-2.6990.2181090.16620710.16921800.9740.9821000.185
2.699-2.9560.2081050.17819060.1820110.9720.981000.204
2.956-3.3030.207950.1717580.17218530.9750.9811000.195
3.303-3.8110.189700.16815530.16916230.9790.9831000.2
3.811-4.660.189700.15613350.15814050.9780.9841000.197
4.66-6.5590.245680.18310500.18611190.970.98299.91060.238
6.559-47.6650.165350.1816380.186750.9810.97999.70370.237

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