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- PDB-3usg: Crystal structure of LeuT bound to L-leucine in space group C2 fr... -

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Basic information

Entry
Database: PDB / ID: 3usg
TitleCrystal structure of LeuT bound to L-leucine 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 / LEUCINE / PHOSPHOCHOLINE / DI(HYDROXYETHYL)ETHER / UNDECANE / Na(+):neurotransmitter symporter (Snf family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 1.2Nov 20, 2013Group: Other
Revision 1.3Sep 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7608
Polymers58,0771
Non-polymers6837
Water1,13563
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)117,52016
Polymers116,1552
Non-polymers1,36614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4200 Å2
ΔGint-22 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.814, 90.859, 81.645
Angle α, β, γ (deg.)90.00, 103.78, 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 , 7 types, 70 molecules

#2: Chemical ChemComp-LEU / LEUCINE


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24
#7: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM NaAc, 30-35% MPD, 5-10%PEG, 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: Apr 25, 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: 2.5→40 Å / Num. all: 74946 / Num. obs: 29352 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 90.4

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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: 2.502→36.674 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1380 5.03 %random
Rwork0.2127 ---
obs0.2136 27415 90.04 %-
all-74946 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.26 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.3376 Å2-0 Å2-9.1458 Å2
2---1.6225 Å2-0 Å2
3----11.7151 Å2
Refinement stepCycle: LAST / Resolution: 2.502→36.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 43 63 4074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014392
X-RAY DIFFRACTIONf_angle_d0.6895644
X-RAY DIFFRACTIONf_dihedral_angle_d9.9731411
X-RAY DIFFRACTIONf_chiral_restr0.049635
X-RAY DIFFRACTIONf_plane_restr0.003682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5018-2.59120.29041000.24861981X-RAY DIFFRACTION69
2.5912-2.69490.29491240.25432341X-RAY DIFFRACTION82
2.6949-2.81750.281210.24022465X-RAY DIFFRACTION85
2.8175-2.9660.30441310.22532565X-RAY DIFFRACTION89
2.966-3.15170.23291240.2152645X-RAY DIFFRACTION92
3.1517-3.39490.26981560.20722716X-RAY DIFFRACTION94
3.3949-3.73620.20321440.19852767X-RAY DIFFRACTION96
3.7362-4.27620.20611580.20332826X-RAY DIFFRACTION98
4.2762-5.38480.20761620.18932843X-RAY DIFFRACTION98
5.3848-36.67740.22241600.22752886X-RAY DIFFRACTION98

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