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- PDB-3qs4: Crystal structure of LeuT mutant F259V bound to sodium and L-tryp... -

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Basic information

Entry
Database: PDB / ID: 3qs4
TitleCrystal structure of LeuT mutant F259V bound to sodium and L-tryptophan
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / NSS / neurotransmitter transporter / LeuT-fold / sodium-coupled secondary transporter / sodium and amino acid binding / membrane
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / TRYPTOPHAN / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.631 Å
AuthorsPiscitelli, C.L. / Gouaux, E.
CitationJournal: Embo J. / Year: 2012
Title: Insights into transport mechanism from LeuT engineered to transport tryptophan.
Authors: Piscitelli, C.L. / Gouaux, E.
History
DepositionFeb 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: 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: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5659
Polymers58,0291
Non-polymers1,5368
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)119,13018
Polymers116,0592
Non-polymers3,07216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area4320 Å2
ΔGint-30 kcal/mol
Surface area38110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.219, 86.595, 82.058
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

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Components

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


Mass: 58029.398 Da / Num. of mol.: 1 / Mutation: F259V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_2077, leut, snf / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.2 M NaCl, 24-26 % PEG-MME 550, 0.05 M L-tryptophan, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 18602 / % possible obs: 99.6 % / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 51.3 Å2 / Rsym value: 0.044 / Net I/σ(I): 16.1
Reflection shellResolution: 2.63→2.74 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1840 / Rsym value: 0.418 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 2010_04_18_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F3A

3f3a


Resolution: 2.631→45.019 Å / SU ML: 0.23 / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.13 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 833 4.94 %RANDOM
Rwork0.214 ---
obs0.2148 16864 89.64 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.188 Å2 / ksol: 0.272 e/Å3
Displacement parametersBiso mean: 68.66 Å2
Baniso -1Baniso -2Baniso -3
1-29.4793 Å2-0 Å2-9.5307 Å2
2---5.4408 Å2-0 Å2
3----24.0386 Å2
Refinement stepCycle: LAST / Resolution: 2.631→45.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 107 33 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024251
X-RAY DIFFRACTIONf_angle_d0.5595773
X-RAY DIFFRACTIONf_dihedral_angle_d11.711469
X-RAY DIFFRACTIONf_chiral_restr0.041657
X-RAY DIFFRACTIONf_plane_restr0.003693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.631-2.79580.30241060.28112155X-RAY DIFFRACTION73
2.7958-3.01170.30191230.25452410X-RAY DIFFRACTION82
3.0117-3.31460.24671350.2372680X-RAY DIFFRACTION90
3.3146-3.79410.23251520.20342837X-RAY DIFFRACTION96
3.7941-4.77930.18541580.18762948X-RAY DIFFRACTION98
4.7793-45.02570.22971590.21413001X-RAY DIFFRACTION99

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