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

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Basic information

Entry
Database: PDB / ID: 3usj
TitleCrystal structure of LeuT bound to L-leucine in space group P21 from lipid bicelles
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / Leucine transporter
Function / homologySodium: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: 3.5 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5098
Polymers116,1552
Non-polymers3546
Water00
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
A: Transporter
hetero molecules

B: 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_546-x,y-1/2,-z+11
Buried area2240 Å2
ΔGint-31 kcal/mol
Surface area35530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.307, 179.880, 57.207
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B

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Components

#1: Protein Transporter


Mass: 58077.438 Da / Num. of mol.: 2
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


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM NaAc, 35% MPD, 5-10% PEG400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: -h,k,l / Fraction: 0.468
ReflectionResolution: 3.5→50 Å / Num. all: 36883 / Num. obs: 13846 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.1
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 83.4

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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 / Resolution: 3.5→48.33 Å / σ(F): 0 / Phase error: 33.75 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3095 725 5.25 %random
Rwork0.2638 ---
obs0.2708 13822 93.84 %-
all-36883 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.069 Å2 / ksol: 0.278 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-90.8954 Å2-0 Å217.3835 Å2
2---42.0289 Å2-0 Å2
3----48.8665 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 22 0 7958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088222
X-RAY DIFFRACTIONf_angle_d0.60911226
X-RAY DIFFRACTIONf_dihedral_angle_d9.5022784
X-RAY DIFFRACTIONf_chiral_restr0.0391270
X-RAY DIFFRACTIONf_plane_restr0.0021362
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3979X-RAY DIFFRACTIONPOSITIONAL
12B3979X-RAY DIFFRACTIONPOSITIONAL0.004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4997-3.76920.40641320.36032388X-RAY DIFFRACTION82
3.7692-4.14730.34631390.31122580X-RAY DIFFRACTION89
4.1473-4.74450.28081430.25692703X-RAY DIFFRACTION92
4.7445-5.96680.28581310.25392694X-RAY DIFFRACTION93
5.9668-26.88960.29841550.22492700X-RAY DIFFRACTION91
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)
10.7044-0.62210.43641.28560.15170.7648-0.0701-0.22880.08850.04890.0487-0.1542-0.01980.131-0.00020.42730.0348-0.13610.3499-0.02960.23119.9707-25.979627.7659
20.6032-0.0001-0.19861.09460.25610.5604-0.17710.02480.0755-0.44340.0491-0.3773-0.0210.2231-0.0751.0287-0.0606-0.28790.1538-0.0797-0.34143.226418.419429.5061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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