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- PDB-5jae: LeuT in the outward-oriented, Na+-free return state, P21 form at ... -

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Basic information

Entry
Database: PDB / ID: 5jae
TitleLeuT in the outward-oriented, Na+-free return state, P21 form at pH 6.5
ComponentsTransporterTransport protein
KeywordsMEMBRANE PROTEIN / neurotransmitter:sodium symporter family / amino acid transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,37113
Polymers116,1552
Non-polymers3,21611
Water79344
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2475
Polymers58,0771
Non-polymers1,1694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1248
Polymers58,0771
Non-polymers2,0477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.570, 92.080, 92.470
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transporter / Transport protein


Mass: 58077.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / 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 / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 11
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 / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 58.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 uL + 1uL drop with 500 uL reservoir solution: 100 mM Tris-MES pH 6.5, 75 mM K-Citrate, 24-28% w/w PEG550 MME and 10% (v/v) glycerol; protein buffer: 10 mM Tris-MES pH 6.0, 100 mM KCl, 10% ...Details: 1 uL + 1uL drop with 500 uL reservoir solution: 100 mM Tris-MES pH 6.5, 75 mM K-Citrate, 24-28% 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: Aug 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→49.3 Å / Num. obs: 46789 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.8 % / % possible all: 98.5

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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: 2.5→46.046 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1000 2.14 %
Rwork0.223 --
obs0.2234 46789 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7971 0 209 44 8224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048433
X-RAY DIFFRACTIONf_angle_d0.62111470
X-RAY DIFFRACTIONf_dihedral_angle_d15.064701
X-RAY DIFFRACTIONf_chiral_restr0.041319
X-RAY DIFFRACTIONf_plane_restr0.0051369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.63190.371380.3756434X-RAY DIFFRACTION98
2.6319-2.79670.33531410.31586497X-RAY DIFFRACTION99
2.7967-3.01260.29591410.27166466X-RAY DIFFRACTION99
3.0126-3.31570.31041450.24916541X-RAY DIFFRACTION99
3.3157-3.79530.25161430.21546544X-RAY DIFFRACTION99
3.7953-4.78090.23471450.19996616X-RAY DIFFRACTION100
4.7809-46.05420.2041470.19936691X-RAY DIFFRACTION100
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)
13.26910.888-0.2071.0728-0.42271.44020.02310.5891-0.11940.0350.16480.33690.23330.0498-0.16580.6697-0.0803-0.08090.7446-0.07980.760923.3183-0.13430.8614
24.7946-0.72221.01431.8981.1181.1988-0.12680.25740.8537-0.1656-0.09880.3031-0.2696-0.32020.27020.54960.00760.03490.67270.11760.686813.640617.519614.1383
32.27720.18650.35130.98970.29041.3128-0.09750.51-0.0146-0.27160.19280.34750.0286-0.1229-0.06370.5852-0.0948-0.03550.75270.05710.72520.96717.18783.4771
42.64180.5002-0.08781.06871.92523.9002-0.18660.36530.1715-0.20790.3906-0.3606-0.4026-0.1251-0.13440.4554-0.05030.07490.6542-0.03280.422339.38979.383710.1465
53.0713-0.9253-1.48781.33890.88822.68470.1296-0.87540.53740.01540.3213-0.620.19480.1862-0.44520.8160.1562-0.18630.7459-0.12230.867162.28737.913545.7475
63.22750.50230.03212.6138-0.70711.7959-0.03-0.01630.13910.23170.1329-0.29930.01910.0333-0.10230.56570.0865-0.03220.5456-0.11180.527757.803612.016929.0962
72.87241.05820.48641.1587-0.60572.10560.1555-0.41940.1690.5201-0.0129-0.2507-0.09740.2685-0.08640.62980.1268-0.05460.6405-0.13450.758465.760114.141739.1039
81.92140.01670.46651.34070.80212.2356-0.0109-0.5403-0.01540.5410.1411-0.01290.21330.0135-0.1970.69150.06190.01760.74660.04980.533846.22696.642641.4884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:93
2X-RAY DIFFRACTION2chain A and resid 94:231
3X-RAY DIFFRACTION3chain A and resid 232:461
4X-RAY DIFFRACTION4chain A and resid 462:512
5X-RAY DIFFRACTION5chain B and resid 4:62
6X-RAY DIFFRACTION6chain B and resid 63:197
7X-RAY DIFFRACTION7chain B and resid 198:383
8X-RAY DIFFRACTION8chain B and resid 384:510

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