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- PDB-3gjc: Crystal Structure of the E290S mutant of LeuT with bound OG -

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Basic information

Entry
Database: PDB / ID: 3gjc
TitleCrystal Structure of the E290S mutant 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: 2.8 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: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Jul 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 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,46914
Polymers114,8212
Non-polymers2,64712
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint3 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.790, 93.510, 87.460
Angle α, β, γ (deg.)90.000, 94.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 5:470 or resseq 478:506 )
21chain B and (resseq 5:470 or resseq 478:506 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLUGLUAA5 - 4705 - 470
12GLUGLUARGARGAA478 - 506478 - 506
21ARGARGGLUGLUBB5 - 4705 - 470
22GLUGLUARGARGBB478 - 506478 - 506

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Components

#1: Protein Transporter / Transport protein / LeuT


Mass: 57410.648 Da / Num. of mol.: 2 / Mutation: E290S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_2077, snf / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#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.: 8
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.: 32 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 150mM NaCl, 100mM Hepes, 23% PEG 550 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9081 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9081 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32597 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 48.5 Å2 / Rsym value: 0.126 / Net I/σ(I): 9.06
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.96 / Num. unique all: 3287 / Rsym value: 0.666 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345165data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2.8→29.204 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.04 / Stereochemistry target values: ML / Details: Phenix_refine
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1033 3.17 %Random
Rwork0.221 ---
obs0.223 32577 97.81 %-
all-33342 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.636 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 212.6 Å2 / Biso mean: 54.081 Å2 / Biso min: 1.54 Å2
Baniso -1Baniso -2Baniso -3
1--6.539 Å2-0 Å2-5.235 Å2
2--0.944 Å20 Å2
3---5.595 Å2
Refine analyzeLuzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 180 32 8106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058318
X-RAY DIFFRACTIONf_angle_d0.90411314
X-RAY DIFFRACTIONf_chiral_restr0.0571260
X-RAY DIFFRACTIONf_plane_restr0.0051354
X-RAY DIFFRACTIONf_dihedral_angle_d19.4582944
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3922X-RAY DIFFRACTIONPOSITIONAL
12B3922X-RAY DIFFRACTIONPOSITIONAL0.031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.9470.3221490.2714497464699
2.947-3.1320.2951460.2454557470399
3.132-3.3740.2671460.2234479462598
3.374-3.7120.291390.2094504464398
3.712-4.2480.2651480.2094547469598
4.248-5.3470.2631400.1984511465198
5.347-29.2060.2211650.2224449461495
Refinement TLS params.Method: refined / Origin x: 0.0427 Å / Origin y: 14.6322 Å / Origin z: -22.0594 Å
111213212223313233
T-0.0419 Å2-0.0068 Å20.0634 Å2--0.266 Å20.055 Å2---0.0892 Å2
L0.0379 °2-0.0483 °2-0.046 °2-0.3329 °20.0441 °2--0.3391 °2
S0.0531 Å °-0.1024 Å °-0.009 Å °0.1173 Å °-0.0134 Å °-0.1437 Å °0.0233 Å °0.3307 Å °0.0651 Å °
Refinement TLS groupSelection details: all

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