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- PDB-3qs6: Crystal structure of LeuT mutant F259V,I359Q bound to sodium and ... -

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Basic information

Entry
Database: PDB / ID: 3qs6
TitleCrystal structure of LeuT mutant F259V,I359Q 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: 2.801 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,1727
Polymers58,0441
Non-polymers1,1276
Water21612
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)118,34314
Polymers116,0892
Non-polymers2,25512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4210 Å2
ΔGint-32 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.793, 87.127, 82.169
Angle α, β, γ (deg.)90.00, 94.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 58044.367 Da / Num. of mol.: 1 / Mutation: F259V,I359Q
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.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.2M NaCl, 20% PEG-MME 550, 0.05M 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15756 / % possible obs: 98.3 % / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 49.15 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.803 / % possible all: 98.6

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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 2A65

2a65


Resolution: 2.801→33.487 Å / SU ML: 0.44 / Isotropic thermal model: individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 715 5 %random
Rwork0.1997 ---
obs0.2018 14291 89.37 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.555 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso mean: 57.67 Å2
Baniso -1Baniso -2Baniso -3
1-25.8881 Å20 Å23.7523 Å2
2---7.4886 Å2-0 Å2
3----18.3994 Å2
Refinement stepCycle: LAST / Resolution: 2.801→33.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 77 12 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024254
X-RAY DIFFRACTIONf_angle_d0.5635773
X-RAY DIFFRACTIONf_dihedral_angle_d12.7631475
X-RAY DIFFRACTIONf_chiral_restr0.041656
X-RAY DIFFRACTIONf_plane_restr0.002696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-3.0170.3141040.24322243X-RAY DIFFRACTION74
3.017-3.32040.27671490.21252544X-RAY DIFFRACTION85
3.3204-3.80030.21931300.18682832X-RAY DIFFRACTION93
3.8003-4.78570.23761670.17382933X-RAY DIFFRACTION97
4.7857-33.48950.21571650.21323024X-RAY DIFFRACTION98

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