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- PDB-7djc: Crystal structure of the G26C/Q250A mutant of LeuT -

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Basic information

Entry
Database: PDB / ID: 7djc
TitleCrystal structure of the G26C/Q250A mutant of LeuT
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / Neurotransmitter transporter / NSS / SLC6
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.701 Å
AuthorsFan, J. / Xiao, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structures of LeuT reveal conformational dynamics in the outward-facing states.
Authors: Fan, J. / Xiao, Y. / Quick, M. / Yang, Y. / Sun, Z. / Javitch, J.A. / Zhou, X.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)57,9115
Polymers57,4421
Non-polymers4704
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint1 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.758, 87.606, 81.813
Angle α, β, γ (deg.)90.000, 94.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 57441.727 Da / Num. of mol.: 1 / Mutation: G26C/Q250A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.05 M Li2SO4, 0.1 M glycine pH 9.0 and 25% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.701→43.803 Å / Num. obs: 17479 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.13 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.063 / Rrim(I) all: 0.117 / Net I/σ(I): 8.1 / Num. measured all: 59165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.701-2.7473.10.62827648860.8020.4240.761.597.9
7.32-43.8033.20.02628188900.9990.0170.03121.696.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2.701→31.508 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 918 5.26 %
Rwork0.2062 16537 -
obs0.208 17455 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.18 Å2 / Biso mean: 63.6895 Å2 / Biso min: 29.61 Å2
Refinement stepCycle: final / Resolution: 2.701→31.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 31 6 3911
Biso mean--72.18 49.22 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.701-2.84280.33981360.2891232998
2.8428-3.02080.27341410.2377234198
3.0208-3.25380.25531470.2177232199
3.2538-3.58080.26681250.2106236599
3.5808-4.0980.22071150.1896239599
4.098-5.15940.22231140.1874239299
5.1594-31.5080.22551400.2051239498
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)
10.6050.4635-0.19920.2828-0.24520.2187-0.1772-0.1597-0.02720.3901-0.0176-0.0251-0.22910.2237-00.53480.0814-0.05230.5566-0.01670.480820.2923-21.817124.4471
20.647-0.20620.58420.35940.32671.0007-0.091-0.06340.07920.04340.035-0.11080.1340.0042-00.38930.02170.01910.3903-0.03680.416310.0677-23.653417.299
31.08110.21530.20211.5641-0.05220.78790.0154-0.2560.01320.3108-0.0359-0.13130.1033-0.0478-00.48870.03830.03220.4875-0.01870.406710.304-28.648726.6993
40.6882-0.07910.0390.78120.01641.2933-0.0698-0.07620.11850.16870.0547-0.00440.08890.146700.37510.0396-0.00850.3552-0.0520.337513.2113-22.01719.9569
50.5396-0.51650.2360.5727-0.34120.294-0.28990.30230.1019-0.02820.4208-0.50880.09320.4344-00.4325-0.0437-0.01250.6213-0.05120.776831.5439-19.146612.315
60.7472-0.13630.19370.18890.15890.2244-0.21150.07350.08760.57010.0706-0.2295-0.04870.2428-0.00010.4234-0.0217-0.02220.39940.050.44796.4278-18.67020.1022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 54 )A5 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 152 )A55 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 254 )A153 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 437 )A255 - 437
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 480 )A438 - 480
6X-RAY DIFFRACTION6chain 'A' and (resid 481 through 601 )A481 - 601

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