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- PDB-3usp: Crystal structure of LeuT in heptyl-beta-D-Selenoglucoside -

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Basic information

Entry
Database: PDB / ID: 3usp
TitleCrystal structure of LeuT in heptyl-beta-D-Selenoglucoside
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 / heptyl 1-seleno-beta-D-glucopyranoside / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2May 8, 2013Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.type / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,36214
Polymers58,0771
Non-polymers3,28413
Water1,78399
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)122,72428
Polymers116,1552
Non-polymers6,56926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4300 Å2
ΔGint-77 kcal/mol
Surface area36990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.697, 86.359, 81.399
Angle α, β, γ (deg.)90.00, 96.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 10 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
#5: Sugar
ChemComp-05L / heptyl 1-seleno-beta-D-glucopyranoside / heptyl 1-seleno-beta-D-glucoside / heptyl 1-seleno-D-glucoside / heptyl 1-seleno-glucoside


Type: D-saccharide / Mass: 341.303 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C13H26O5Se

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Non-polymers , 4 types, 103 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-NaOH, 18-22% PEG 550 MME, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 175633 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 94.4

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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: 2.1→47.556 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1892 5.63 %random
Rwork0.2225 ---
obs0.223 64371 90.8 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.065 Å2 / ksol: 0.432 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.7071 Å2-0 Å2-3.9413 Å2
2---8.5078 Å2-0 Å2
3----4.1994 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 147 99 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124525
X-RAY DIFFRACTIONf_angle_d0.5785819
X-RAY DIFFRACTIONf_dihedral_angle_d14.6441448
X-RAY DIFFRACTIONf_chiral_restr0.041669
X-RAY DIFFRACTIONf_plane_restr0.002686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.12780.35631060.2791906X-RAY DIFFRACTION74
2.1278-2.1570.30421240.26642030X-RAY DIFFRACTION78
2.157-2.18780.30091200.26912006X-RAY DIFFRACTION79
2.1878-2.22040.28071220.2582137X-RAY DIFFRACTION83
2.2204-2.25510.29291320.25532137X-RAY DIFFRACTION84
2.2551-2.29210.27241330.23972240X-RAY DIFFRACTION86
2.2921-2.33160.2861300.232215X-RAY DIFFRACTION87
2.3316-2.3740.20861330.2292217X-RAY DIFFRACTION87
2.374-2.41970.24291330.22382295X-RAY DIFFRACTION89
2.4197-2.46910.25131410.22662342X-RAY DIFFRACTION89
2.4691-2.52270.24471340.21832319X-RAY DIFFRACTION91
2.5227-2.58140.24561460.23192340X-RAY DIFFRACTION92
2.5814-2.6460.24681310.2272339X-RAY DIFFRACTION92
2.646-2.71750.26771460.21692426X-RAY DIFFRACTION93
2.7175-2.79750.22691470.22992402X-RAY DIFFRACTION94
2.7975-2.88770.27651420.22112413X-RAY DIFFRACTION94
2.8877-2.99090.23191490.22252467X-RAY DIFFRACTION96
2.9909-3.11070.27721420.2222464X-RAY DIFFRACTION96
3.1107-3.25220.22471440.2182452X-RAY DIFFRACTION96
3.2522-3.42360.25521540.2192488X-RAY DIFFRACTION97
3.4236-3.63810.221550.20562501X-RAY DIFFRACTION97
3.6381-3.91880.21031520.20312530X-RAY DIFFRACTION98
3.9188-4.3130.21151500.19822495X-RAY DIFFRACTION98
4.313-4.93650.17271550.19022506X-RAY DIFFRACTION98
4.9365-6.21730.17891530.23832543X-RAY DIFFRACTION98
6.2173-47.56790.23361500.2422537X-RAY DIFFRACTION99

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