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- PDB-3usk: Crystal structure of LeuT bound to L-leucine in space group P21 f... -

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Basic information

Entry
Database: PDB / ID: 3usk
TitleCrystal structure of LeuT bound to L-leucine in space group P21 from lipid bicelles
ComponentsTransporterTransport protein
KeywordsTRANSPORT PROTEIN / Leucine transporter
Function / homologynitrogen compound transport / Sodium: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 / Resolution: 4.5 Å
AuthorsWang, H. / Elferich, J. / Gouaux, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context.
Authors: Wang, H. / Elferich, J. / Gouaux, E.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
B: Transporter
C: Transporter
D: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,01816
Polymers232,3104
Non-polymers70912
Water0
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2554
Polymers58,0771
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2554
Polymers58,0771
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2554
Polymers58,0771
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2554
Polymers58,0771
Non-polymers1773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Transporter
hetero molecules

C: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5098
Polymers116,1552
Non-polymers3546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2230 Å2
ΔGint-31 kcal/mol
Surface area35370 Å2
MethodPISA
6
B: Transporter
hetero molecules

D: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5098
Polymers116,1552
Non-polymers3546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2270 Å2
ΔGint-32 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 112.483, 165.320
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B
311chain C
411chain D

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Components

#1: Protein
Transporter / Transport protein


Mass: 58077.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf, aq_2077 / 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.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na

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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: 55.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100mM NaAc, 36% MPD, 10% PEG400, 50 mM MgCl2, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. all: 27450 / Num. obs: 12873 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.55
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / % possible all: 80.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata 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 2A65

2a65


Resolution: 4.5→19.905 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 611 5.03 %
Rwork0.2652 --
obs0.2654 12153 79.2 %
all-27450 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.743 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.3338 Å20 Å2-3.1439 Å2
2--23.0324 Å20 Å2
3----36.3662 Å2
Refinement stepCycle: LAST / Resolution: 4.5→19.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15871 0 44 0 15915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816444
X-RAY DIFFRACTIONf_angle_d0.51822452
X-RAY DIFFRACTIONf_dihedral_angle_d9.5595568
X-RAY DIFFRACTIONf_chiral_restr0.0362540
X-RAY DIFFRACTIONf_plane_restr0.0022724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3979X-RAY DIFFRACTIONPOSITIONAL
12B3979X-RAY DIFFRACTIONPOSITIONAL0.004
13C3979X-RAY DIFFRACTIONPOSITIONAL0.002
14D3979X-RAY DIFFRACTIONPOSITIONAL0.004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4782-4.92260.2661420.29372636X-RAY DIFFRACTION73
4.9226-5.62090.30121480.2882890X-RAY DIFFRACTION80
5.6209-7.02950.32721710.29793005X-RAY DIFFRACTION83
7.0295-19.90560.22411500.22113011X-RAY DIFFRACTION82

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