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- PDB-3tt1: Crystal Structure of LeuT in the outward-open conformation in com... -

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Basic information

Entry
Database: PDB / ID: 3tt1
TitleCrystal Structure of LeuT in the outward-open conformation in complex with Fab
Components
  • (mouse monoclonal 1gG2a Fab fragment, ...) x 2
  • Leucine transporter LeuT
KeywordsTRANSPORT PROTEIN / LeuT fold / transporter / plasma membrane
Function / homology
Function and homology information


sodium ion transmembrane transport / membrane
Similarity search - Function
Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Na(+):neurotransmitter symporter (Snf family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsKrishnamurthy, H. / Gouaux, E.
CitationJournal: Nature / Year: 2012
Title: X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.
Authors: Krishnamurthy, H. / Gouaux, E.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Feb 1, 2012Group: Database references
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 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: Leucine transporter LeuT
B: Leucine transporter LeuT
L: mouse monoclonal 1gG2a Fab fragment, heavy chain
H: mouse monoclonal 1gG2a Fab fragment, kappa light chain
M: mouse monoclonal 1gG2a Fab fragment, heavy chain
I: mouse monoclonal 1gG2a Fab fragment, kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,61415
Polymers210,9806
Non-polymers1,6349
Water50428
1
A: Leucine transporter LeuT
M: mouse monoclonal 1gG2a Fab fragment, heavy chain
I: mouse monoclonal 1gG2a Fab fragment, kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4618
Polymers105,4903
Non-polymers9715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine transporter LeuT
L: mouse monoclonal 1gG2a Fab fragment, heavy chain
H: mouse monoclonal 1gG2a Fab fragment, kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1537
Polymers105,4903
Non-polymers6634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.859, 162.761, 210.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 6:129 or resseq 135:308 or resseq 310:471 or resseq 480:507 )
211chain B and (resseq 6:129 or resseq 135:308 or resseq 310:471 or resseq 480:507 )
112chain L and (resseq 21:215 )
212chain M and (resseq 21:215 )
113chain H and (resseq 20:135 or resseq 143:154 or resseq 162:219 )
213chain I and (resseq 20:135 or resseq 143:154 or resseq 162:219 )

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules LMHI

#2: Antibody mouse monoclonal 1gG2a Fab fragment, heavy chain


Mass: 23911.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody mouse monoclonal 1gG2a Fab fragment, kappa light chain


Mass: 23575.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 7 molecules AB

#1: Protein Leucine transporter LeuT


Mass: 58003.336 Da / Num. of mol.: 2 / Mutation: Y108F, K288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O67854
#5: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside / N-Octyl beta-D-thioglucopyranoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 2 types, 32 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40 mM Tris-HCl, 23-26% PEG550 MME, 50-100 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. all: 64779 / Num. obs: 57718 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.9
Reflection shellResolution: 3.099→3.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.92 / Num. unique all: 5864 / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F3A

3f3a


Resolution: 3.099→40.169 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2948 5.11 %RANDOM
Rwork0.2192 ---
obs0.2203 57680 89.09 %-
all-0 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.982 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso mean: 81 Å2
Baniso -1Baniso -2Baniso -3
1--5.1878 Å20 Å2-0 Å2
2--7.6738 Å2-0 Å2
3----2.486 Å2
Refinement stepCycle: LAST / Resolution: 3.099→40.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14178 0 68 28 14274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814661
X-RAY DIFFRACTIONf_angle_d0.94419984
X-RAY DIFFRACTIONf_dihedral_angle_d9.6445005
X-RAY DIFFRACTIONf_chiral_restr0.0542268
X-RAY DIFFRACTIONf_plane_restr0.0022482
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3762X-RAY DIFFRACTIONPOSITIONAL
12B3762X-RAY DIFFRACTIONPOSITIONAL0.008
21L1515X-RAY DIFFRACTIONPOSITIONAL
22M1515X-RAY DIFFRACTIONPOSITIONAL0.007
31H1419X-RAY DIFFRACTIONPOSITIONAL
32I1419X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.099-3.15030.33221350.32572561X-RAY DIFFRACTION89
3.1503-3.20460.36711490.30732703X-RAY DIFFRACTION92
3.2046-3.26280.33431230.29252642X-RAY DIFFRACTION92
3.2628-3.32550.30391390.2892669X-RAY DIFFRACTION92
3.3255-3.39340.32391600.27262631X-RAY DIFFRACTION92
3.3934-3.46710.30291430.25792599X-RAY DIFFRACTION91
3.4671-3.54770.27381440.24592690X-RAY DIFFRACTION91
3.5477-3.63640.23621550.23212595X-RAY DIFFRACTION91
3.6364-3.73470.28661420.22742612X-RAY DIFFRACTION91
3.7347-3.84450.21971510.22722637X-RAY DIFFRACTION90
3.8445-3.96840.27091330.21522626X-RAY DIFFRACTION90
3.9684-4.11010.21731420.20542598X-RAY DIFFRACTION90
4.1101-4.27450.20511500.20662600X-RAY DIFFRACTION89
4.2745-4.46880.23051270.18422610X-RAY DIFFRACTION89
4.4688-4.70410.18921170.17592601X-RAY DIFFRACTION88
4.7041-4.99830.1921430.17582574X-RAY DIFFRACTION88
4.9983-5.38340.19541500.18182552X-RAY DIFFRACTION87
5.3834-5.92360.24031270.22042567X-RAY DIFFRACTION87
5.9236-6.77720.25441110.23242596X-RAY DIFFRACTION86
6.7772-8.52520.21461520.19822534X-RAY DIFFRACTION85
8.5252-40.17260.23251550.22252535X-RAY DIFFRACTION81
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)
11.14330.14620.25161.51220.14341.38710.0106-0.2396-0.05840.1929-0.07520.263-0.0847-0.2934-0.0020.26580.0365-0.00030.3637-0.0360.3207-71.682833.601110.2436
22.1456-0.0972-0.53951.18860.12332.20090.03010.50590.2418-0.3448-0.10180.2379-0.2748-0.5768-0.00530.48270.1426-0.04580.5799-0.14130.5257-74.784128.7768-38.3005
31.9361-0.8019-1.25981.79110.99161.65970.066-0.29470.22120.13850.05760.07380.05440.27160.00020.6034-0.04080.04830.5727-0.18750.4783-29.829712.9909-43.0863
41.098-0.53860.36540.71480.11230.2342-0.1717-0.52690.06830.20850.225-0.3755-0.01460.288100.6110.0310.05050.7529-0.18280.8104-4.73630.5465-54.3015
51.3995-0.71211.18571.3259-1.15711.83210.32030.275-0.2452-0.3729-0.17640.18850.30940.151300.7631-0.0163-0.15410.58430.04070.5501-40.5278-2.280215.2034
60.4448-0.2704-0.10990.59030.37070.22750.42450.2977-0.3847-0.4499-0.25190.00860.27160.1810.00010.91550.2143-0.13810.7586-0.02610.8367-19.1702-20.36926.4751
71.24150.0223-0.05692.31260.35921.2335-0.2490.0149-0.29270.1124-0.07050.13020.15230.1214-00.607-0.05740.1040.502-0.11630.5285-34.3317-3.2742-51.7768
80.78030.2766-0.57250.94450.57511.1012-0.5259-1.434-1.2380.55540.5196-0.40260.25320.21360.00040.89380.29980.10630.9580.23721.0436-5.467-15.5739-47.4483
91.5127-0.0676-0.21081.11590.2521.1133-0.040.31230.23550.0359-0.095-0.17990.24130.180500.5246-0.0099-0.06140.49450.13460.4991-26.69778.295722.9785
100.69780.39740.33361.0801-0.77561.25170.29240.9151-0.0528-0.8868-0.1527-0.76270.37250.53730.00120.92720.34940.18831.07670.07910.7565-4.7465-14.127818.685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:507)
2X-RAY DIFFRACTION2(chain B and resid 6:507)
3X-RAY DIFFRACTION3(chain H and resid 20:142)
4X-RAY DIFFRACTION4(chain H and resid 143:238)
5X-RAY DIFFRACTION5(chain I and resid 20:142)
6X-RAY DIFFRACTION6(chain I and resid 143:238)
7X-RAY DIFFRACTION7(chain L and resid 21:131)
8X-RAY DIFFRACTION8(chain L and resid 132:235)
9X-RAY DIFFRACTION9(chain M and resid 21:131)
10X-RAY DIFFRACTION10(chain M and resid 132:235)

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