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- PDB-8ft4: Multicrystal structure of Na+, leucine-bound LeuT determined at 5 keV -

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Basic information

Entry
Database: PDB / ID: 8ft4
TitleMulticrystal structure of Na+, leucine-bound LeuT determined at 5 keV
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / amino acid transporter / anomalous diffraction / element identification / multiple crystals
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsKarasawa, A. / Liu, H. / Quick, M. / Hendrickson, A.H. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116799 United States
CitationJournal: To be Published
Title: Crystallographic characterization of sodium ions in a bacterial leucine/sodium symporter
Authors: Karasawa, A. / Liu, H. / Quick, M. / Hendrickson, W.A. / Liu, Q.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,32112
Polymers58,3191
Non-polymers2,00211
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.110, 86.383, 80.730
Angle α, β, γ (deg.)90.000, 95.533, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-611-

CL

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Components

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Protein / Sugars , 2 types, 7 molecules A

#1: Protein Na(+):neurotransmitter symporter (Snf family)


Mass: 58318.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#5: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 103 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.0, 100 mM sodium chloride, 20-25% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 2.479 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.479 Å / Relative weight: 1
ReflectionResolution: 4→39.79 Å / Num. obs: 10240 / % possible obs: 99.65 % / Redundancy: 116 % / Biso Wilson estimate: 60.79 Å2 / CC1/2: 0.997 / Net I/σ(I): 26.6
Reflection shellResolution: 4.001→4.144 Å / Num. unique obs: 1028 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSv1-1545data reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GJD

3gjd


Resolution: 4→39.79 Å / SU ML: 0.4748 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 19.5504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 394 3.99 %
Rwork0.1528 9490 -
obs0.1549 9884 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.71 Å2
Refinement stepCycle: LAST / Resolution: 4→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 122 98 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364276
X-RAY DIFFRACTIONf_angle_d0.66085808
X-RAY DIFFRACTIONf_chiral_restr0.0427665
X-RAY DIFFRACTIONf_plane_restr0.0047693
X-RAY DIFFRACTIONf_dihedral_angle_d13.4818584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.580.24411300.14393172X-RAY DIFFRACTION99.88
4.58-5.770.19261680.14583141X-RAY DIFFRACTION99.94
5.77-39.790.1986960.16513177X-RAY DIFFRACTION99.57

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