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- PDB-5jag: LeuT T354H mutant in the outward-oriented, Na+-free Return State -

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Basic information

Entry
Database: PDB / ID: 5jag
TitleLeuT T354H mutant in the outward-oriented, Na+-free Return State
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / NSS family / apo state
Function / homologynitrogen compound transport / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMalinauskaite, L. / Sahin, C. / Said, S. / Grouleff, J. / Shahsavar, A. / Bjerregaard, H. / Noer, P. / Severinsen, K. / Boesen, T. / Schiott, B. ...Malinauskaite, L. / Sahin, C. / Said, S. / Grouleff, J. / Shahsavar, A. / Bjerregaard, H. / Noer, P. / Severinsen, K. / Boesen, T. / Schiott, B. / Sinning, S. / Nissen, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Lundbeck Foundation2012-12576 Denmark
CitationJournal: Nat Commun / Year: 2016
Title: A conserved leucine occupies the empty substrate site of LeuT in the Na(+)-free return state.
Authors: Malinauskaite, L. / Said, S. / Sahin, C. / Grouleff, J. / Shahsavar, A. / Bjerregaard, H. / Noer, P. / Severinsen, K. / Boesen, T. / Schitt, B. / Sinning, S. / Nissen, P.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1618
Polymers58,1141
Non-polymers2,0477
Water1629
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint28 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.230, 95.610, 83.700
Angle α, β, γ (deg.)90.00, 97.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter


Mass: 58114.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Gene: snf, aq_2077 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): c41 / References: UniProt: O67854
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 uL + 1uL drop with 500 uL reservoir solution: 100 mM Tris-MES pH 5.5, 100 mM KCl, 20-24% w/w PEG550 MME and 10% (v/v) glycerol; protein buffer: 10 mM Tris-MES pH 6.0, 100 mM KCl, 10% (v/v) ...Details: 1 uL + 1uL drop with 500 uL reservoir solution: 100 mM Tris-MES pH 5.5, 100 mM KCl, 20-24% w/w PEG550 MME and 10% (v/v) glycerol; protein buffer: 10 mM Tris-MES pH 6.0, 100 mM KCl, 10% (v/v) glycerol, 40 mM n-octyl-beta-D-glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.58→36.7 Å / Num. obs: 21133 / % possible obs: 99.9 % / Redundancy: 2.2 % / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 2.58→2.69 Å / Mean I/σ(I) obs: 1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F3A

3f3a


Resolution: 2.58→36.663 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 999 4.73 %
Rwork0.2192 --
obs0.2208 21134 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→36.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 140 9 4072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024187
X-RAY DIFFRACTIONf_angle_d0.5085689
X-RAY DIFFRACTIONf_dihedral_angle_d13.2982323
X-RAY DIFFRACTIONf_chiral_restr0.037659
X-RAY DIFFRACTIONf_plane_restr0.004671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5802-2.71620.38491440.36412900X-RAY DIFFRACTION98
2.7162-2.88630.34811430.30682879X-RAY DIFFRACTION98
2.8863-3.1090.32341420.27272874X-RAY DIFFRACTION98
3.109-3.42170.31271450.24192906X-RAY DIFFRACTION98
3.4217-3.91640.21661420.20722875X-RAY DIFFRACTION98
3.9164-4.93230.24771420.18672863X-RAY DIFFRACTION96
4.9323-36.66640.21031410.19482838X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.23581.0075-1.07011.0505-0.12963.6667-0.0178-0.07820.0614-0.02150.0421-0.1163-0.39270.51260.00310.6951-0.00580.00240.5138-0.0690.480613.0035-2.365921.1138
22.19260.37131.43123.2516-0.94316.4720.1467-0.3617-0.21580.239-0.07570.0350.4802-0.0685-0.12020.40880.01340.15690.5259-0.00790.43662.8243-12.967328.7847
31.4562-0.0178-0.11922.173-0.81333.1571-0.1541-0.2380.11010.15080.0401-0.3922-0.39080.59010.12830.6377-0.0106-0.00520.5562-0.09650.476614.125-3.921422.3376
47.84820.51474.2461.260.21835.83180.29360.1759-0.1961-0.16260.0825-0.38170.04570.5619-0.35450.6616-0.08190.13290.5383-0.01650.458616.1753-4.67375.306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:139
2X-RAY DIFFRACTION2chain A and resid 140:231
3X-RAY DIFFRACTION3chain A and resid 232:450
4X-RAY DIFFRACTION4chain A and resid 451:507

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