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- PDB-8s4j: Structure, substrate selectivity determinants and membrane intera... -

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Basic information

Entry
Database: PDB / ID: 8s4j
TitleStructure, substrate selectivity determinants and membrane interactions of a Glutamate-specific TAXI TRAP binding protein from Vibrio cholerae.
ComponentsTAXI family TRAP transporter solute-binding subunit
KeywordsTRANSPORT PROTEIN / Substrate binding protein TAXI-TRAP Glutamate Periplasmic
Function / homologyTRAP transporter solute receptor, TAXI family / NMT1-like family / GLUTAMIC ACID / TAXI family TRAP transporter solute-binding subunit
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMulligan, C. / Daab, A. / Davies, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V007424/1 United Kingdom
CitationJournal: J.Gen.Physiol. / Year: 2024
Title: Structure and selectivity of a glutamate-specific TAXI TRAP binding protein from Vibrio cholerae.
Authors: Davies, J.F.S. / Daab, A. / Massouh, N. / Kirkland, C. / Strongitharm, B. / Leech, A. / Farre, M. / Thomas, G.H. / Mulligan, C.
History
DepositionFeb 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAXI family TRAP transporter solute-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8217
Polymers32,5591
Non-polymers2626
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-35 kcal/mol
Surface area12210 Å2
Unit cell
Length a, b, c (Å)126.660, 126.660, 180.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein TAXI family TRAP transporter solute-binding subunit


Mass: 32558.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: D6U24_12840, I7465_15265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H6LKE4
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Angstroms
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→69.64 Å / Num. obs: 61144 / % possible obs: 99.99 % / Redundancy: 20.5 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06415 / Rpim(I) all: 0.01456 / Rrim(I) all: 0.0658 / Net I/σ(I): 26.31
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 0.9057 / Mean I/σ(I) obs: 3.42 / Num. unique obs: 6061 / CC1/2: 0.917 / Rrim(I) all: 0.2063

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
DIMPLEv2.6.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→69.64 Å / SU ML: 0.2557 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7765
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 3035 4.96 %
Rwork0.1902 58105 -
obs0.1914 61140 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 15 258 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682503
X-RAY DIFFRACTIONf_angle_d0.96393425
X-RAY DIFFRACTIONf_chiral_restr0.0624379
X-RAY DIFFRACTIONf_plane_restr0.0063455
X-RAY DIFFRACTIONf_dihedral_angle_d6.0741375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.39231470.39272604X-RAY DIFFRACTION99.96
1.73-1.750.32591440.34342627X-RAY DIFFRACTION100
1.75-1.790.34071290.3062610X-RAY DIFFRACTION100
1.79-1.820.30451190.27152624X-RAY DIFFRACTION100
1.82-1.850.27591320.25882651X-RAY DIFFRACTION100
1.85-1.890.28141360.23242620X-RAY DIFFRACTION100
1.89-1.930.26941440.22882633X-RAY DIFFRACTION100
1.93-1.980.26371280.21882615X-RAY DIFFRACTION100
1.98-2.030.26611420.21162599X-RAY DIFFRACTION100
2.03-2.080.22111290.21752634X-RAY DIFFRACTION100
2.08-2.140.24521370.22632623X-RAY DIFFRACTION100
2.14-2.210.27021520.23782626X-RAY DIFFRACTION99.96
2.21-2.290.22671560.20182606X-RAY DIFFRACTION100
2.29-2.380.21761290.19742636X-RAY DIFFRACTION100
2.38-2.490.21261550.20352633X-RAY DIFFRACTION100
2.49-2.620.23691490.21212629X-RAY DIFFRACTION100
2.62-2.790.23621360.21832656X-RAY DIFFRACTION100
2.79-30.25041460.21562631X-RAY DIFFRACTION100
3-3.30.21791230.18612674X-RAY DIFFRACTION100
3.3-3.780.17921320.15562684X-RAY DIFFRACTION100
3.78-4.760.12911310.1252701X-RAY DIFFRACTION100
4.76-69.640.17141390.1582789X-RAY DIFFRACTION99.86

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