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- PDB-3gjd: Crystal Structure of LeuT with bound OG -

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Basic information

Entry
Database: PDB / ID: 3gjd
TitleCrystal Structure of LeuT with bound OG
ComponentsTransporterTransport protein
KeywordsTRANSPORT PROTEIN / Transmembrane transport / neurotransmitter:sodium symport / Sodium-coupled transport / NSS / aminoacid transport / Symport / Transmembrane / Transport
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 / molecular replacement / Resolution: 2 Å
AuthorsWinther, A.M.L. / Quick, M. / Javitch, J.A. / Nissen, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation
Authors: Quick, M. / Winther, A.M.L. / Shi, L. / Nissen, P. / Weinstein, H. / Javitch, J.A.
History
DepositionMar 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 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 / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 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: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57811
Polymers57,6111
Non-polymers1,96710
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,15522
Polymers115,2222
Non-polymers3,93420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7010 Å2
ΔGint-19 kcal/mol
Surface area38760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.510, 86.570, 81.290
Angle α, β, γ (deg.)90.000, 95.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 7 molecules A

#1: Protein Transporter / Transport protein / LeuT


Mass: 57610.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / 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: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 102 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 150mM NaCl, 100mM Hepes, 23% PEG 550 MME, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2008
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 39607 / Num. obs: 39607 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 30.25 Å2 / Rsym value: 0.078 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.75 / Num. unique all: 5328 / Rsym value: 0.644 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2→29.553 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.01 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.28 / Stereochemistry target values: ML / Details: Phenix_refine
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2000 5.05 %Random
Rwork0.169 ---
obs0.171 39602 97.02 %-
all-40838 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.308 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 147.61 Å2 / Biso mean: 40.304 Å2 / Biso min: 16.67 Å2
Baniso -1Baniso -2Baniso -3
1-7.343 Å2-0 Å2-4.178 Å2
2---5.766 Å2-0 Å2
3----2.679 Å2
Refine analyzeLuzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 121 98 4263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064287
X-RAY DIFFRACTIONf_angle_d0.9195823
X-RAY DIFFRACTIONf_chiral_restr0.062642
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d20.2891544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.2511430.2132686282996
2.05-2.1050.2391390.1922623276296
2.105-2.1670.2171410.1672638277996
2.167-2.2370.21410.1572664280597
2.237-2.3170.2151410.1562659280097
2.317-2.410.2061440.1482681282597
2.41-2.520.181410.1512681282297
2.52-2.6520.2161440.1552690283497
2.652-2.8180.2071430.1542682282597
2.818-3.0360.2231420.1562695283797
3.036-3.3410.1951440.1642688283297
3.341-3.8230.191450.1572717286298
3.823-4.8140.1711440.1642724286898
4.814-29.5570.1881480.1852774292298
Refinement TLS params.Method: refined / Origin x: 26.3589 Å / Origin y: 29.735 Å / Origin z: 21.6284 Å
111213212223313233
T0.1743 Å20.0242 Å20.0124 Å2-0.1848 Å20.0055 Å2--0.1818 Å2
L0.6985 °2-0.179 °20.1302 °2-0.7723 °20.1747 °2--0.8123 °2
S-0.0656 Å °0.0538 Å °-0.0071 Å °0.0041 Å °0.0165 Å °0.0898 Å °-0.0417 Å °-0.0414 Å °0 Å °
Refinement TLS groupSelection details: all

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