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- PDB-7dj2: Crystal structure of the G26C/E290S mutant of LeuT -

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Basic information

Entry
Database: PDB / ID: 7dj2
TitleCrystal structure of the G26C/E290S 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 / membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 19, 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)
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8078
Polymers114,9132
Non-polymers8936
Water3,729207
1
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9034
Polymers57,4571
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint1 kcal/mol
Surface area19410 Å2
MethodPISA
2
B: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9034
Polymers57,4571
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint2 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.327, 110.707, 87.135
Angle α, β, γ (deg.)90.000, 96.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57456.742 Da / Num. of mol.: 2 / Mutation: G26C/E290S
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 / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / 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 / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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.: 207 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Mg2+-formate dihydrate, 0.1 M Na+-MOPS pH 7.0, 17% (w/v) PEG 3350 and 15% (v/v) glycerol

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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: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→46.649 Å / Num. obs: 60625 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.08 / Rrim(I) all: 0.151 / Net I/σ(I): 6.8 / Num. measured all: 208585
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
2.4-2.4423.20.698947629870.730.4660.8421.699.7
6.51-46.6493.30.0491025330870.9960.0320.05818.498.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2a65


Resolution: 2.4→43.329 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2999 4.95 %
Rwork0.2117 57579 -
obs0.213 60578 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.14 Å2 / Biso mean: 44.9052 Å2 / Biso min: 22.94 Å2
Refinement stepCycle: final / Resolution: 2.4→43.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7827 0 60 207 8094
Biso mean--58.51 47.82 -
Num. residues----986
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4002-2.43950.29551440.28262712100
2.4395-2.48160.3021500.26172736100
2.4816-2.52670.26851420.25362705100
2.5267-2.57530.28351580.24982764100
2.5753-2.62790.27171440.24372713100
2.6279-2.6850.26531100.23882758100
2.685-2.74750.24951490.23232727100
2.7475-2.81620.24791620.22322718100
2.8162-2.89230.23341440.22352714100
2.8923-2.97740.2721320.21432765100
2.9774-3.07350.26481340.21642771100
3.0735-3.18330.2551630.2252698100
3.1833-3.31070.24831460.21482746100
3.3107-3.46130.22931350.20692766100
3.4613-3.64370.24481480.19982725100
3.6437-3.87190.21381380.20352736100
3.8719-4.17060.24941220.20472803100
4.1706-4.58990.24731430.19862752100
4.5899-5.2530.20671440.18012748100
5.253-6.61450.24781360.21642780100
6.6145-43.3290.18211550.1936274297
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)
11.16630.5122-0.3930.8902-0.43571.4970.0757-0.02970.08780.10690.0180.0211-0.1053-0.0022-0.09680.25420.0207-0.02120.26010.00550.4017-8.455718.5647-8.8538
21.29450.66640.06381.1166-0.15870.66320.0771-0.0462-0.01630.1218-0.0015-0.0689-0.00850.0222-0.06720.22470.0332-0.01750.2257-0.02280.3375-4.638920.5643-11.5076
32.4509-0.02052.22831.3967-0.67033.90490.146-0.3714-0.16720.47960.03520.24910.046-0.3369-0.1660.3392-0.00270.10090.31040.01680.3856-21.011112.56311.2511
42.6432.14512.02034.42071.61.5449-1.8725-1.7574-1.0095-1.66090.1621-0.90870.0813-2.62311.75880.53820.08120.03320.65390.06140.2693-7.86618.2059-8.1417
51.0044-0.6649-0.31451.37280.47520.81490.11640.10110.087-0.159-0.056-0.0188-0.067-0.1007-0.04890.2567-0.0143-0.010.3238-0.0110.4682-46.79889.6389-37.1568
61.2579-0.28840.13521.41550.1380.76170.09820.1768-0.0298-0.1747-0.0970.10410.0077-0.0584-0.0090.2409-0.01-0.00260.32680.00770.3675-50.857813.2573-36.0746
71.85710.9182.01492.69952.03032.88360.10830.1854-0.1745-0.23650.0047-0.17630.08540.0926-0.13470.22060.00680.06530.3259-0.02650.4117-34.11550.4184-42.5803
86.6617-6.19681.57996.3257-0.47492.1375-1.50370.6276-1.68140.50832.2972.7826-1.11820.2566-0.80540.47870.01320.17420.691-0.01690.8672-47.57879.5834-37.371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 152 )A5 - 152
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 409 )A153 - 409
3X-RAY DIFFRACTION3chain 'A' and (resid 410 through 508 )A410 - 508
4X-RAY DIFFRACTION4chain 'A' and (resid 601 through 601 )A601
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 152 )B5 - 152
6X-RAY DIFFRACTION6chain 'B' and (resid 153 through 409 )B153 - 409
7X-RAY DIFFRACTION7chain 'B' and (resid 410 through 508 )B410 - 508
8X-RAY DIFFRACTION8chain 'B' and (resid 601 through 601 )B601

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