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- PDB-8ft5: Crystal structure of LeuT soaked with Crown-5 -

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Basic information

Entry
Database: PDB / ID: 8ft5
TitleCrystal structure of LeuT soaked with Crown-5
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 / plasma membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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)58,5315
Polymers58,3191
Non-polymers2134
Water00
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)86.442, 87.383, 80.798
Angle α, β, γ (deg.)90.000, 95.062, 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

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Components

#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
#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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.64 Å3/Da / Density % sol: 53.38 %
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: 3.8→39.44 Å / Num. obs: 7654 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 122.34 Å2 / CC1/2: 0.982 / Net I/σ(I): 2.3
Reflection shellResolution: 3.8→3.936 Å / Num. unique obs: 594 / CC1/2: 0.535

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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: 3.8→39.44 Å / SU ML: 0.5518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3127 588 9.95 %
Rwork0.2712 5320 -
obs0.2753 5908 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.9 Å2
Refinement stepCycle: LAST / Resolution: 3.8→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 12 0 4045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214168
X-RAY DIFFRACTIONf_angle_d0.49665676
X-RAY DIFFRACTIONf_chiral_restr0.0393640
X-RAY DIFFRACTIONf_plane_restr0.004693
X-RAY DIFFRACTIONf_dihedral_angle_d13.75921427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.180.39371470.35671321X-RAY DIFFRACTION98.72
4.18-4.790.361450.28861321X-RAY DIFFRACTION98.19
4.79-6.030.31611470.28691314X-RAY DIFFRACTION98.72
6.03-39.440.26211490.23111364X-RAY DIFFRACTION98.76

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