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- PDB-3usl: Crystal Structure of LeuT bound to L-selenomethionine in space gr... -

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Basic information

Entry
Database: PDB / ID: 3usl
TitleCrystal Structure of LeuT bound to L-selenomethionine in space group C2 from lipid bicelles
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / Leucine transporter
Function / homology
Function and homology information


sodium ion transmembrane transport / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
ACETATE ION / IODIDE ION / SELENOMETHIONINE / PHOSPHOCHOLINE / Na(+):neurotransmitter symporter (Snf family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6907
Polymers58,0771
Non-polymers6126
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,37914
Polymers116,1552
Non-polymers1,22412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.323, 90.062, 81.968
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transporter


Mass: 58077.438 Da / Num. of mol.: 1
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) / References: UniProt: O67854

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Non-polymers , 6 types, 30 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2Se
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM NaAc, 35% MPD, 10%PEG, 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: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2011
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.71→40 Å / Num. obs: 23553 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.71→2.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.4 / % possible all: 92.2

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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: 2.71→37.156 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1165 5.16 %random
Rwork0.2124 ---
obs0.214 22577 94.51 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.099 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.3929 Å2-0 Å2-13.6978 Å2
2--2.8867 Å2-0 Å2
3----14.2796 Å2
Refinement stepCycle: LAST / Resolution: 2.71→37.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 27 24 4019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014378
X-RAY DIFFRACTIONf_angle_d0.6475627
X-RAY DIFFRACTIONf_dihedral_angle_d9.5771398
X-RAY DIFFRACTIONf_chiral_restr0.047634
X-RAY DIFFRACTIONf_plane_restr0.003682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6981-2.82080.26761290.24132311X-RAY DIFFRACTION82
2.8208-2.96950.26811340.22532534X-RAY DIFFRACTION91
2.9695-3.15540.25231390.23252668X-RAY DIFFRACTION94
3.1554-3.39890.28031680.21682674X-RAY DIFFRACTION97
3.3989-3.74070.22661320.20132773X-RAY DIFFRACTION97
3.7407-4.28130.2381450.21392811X-RAY DIFFRACTION99
4.2813-5.39130.20541450.20022834X-RAY DIFFRACTION99
5.3913-37.15920.25961730.21282807X-RAY DIFFRACTION98

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