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- PDB-4mm6: Crystal structure of LeuBAT (delta13 mutant) in complex with (S)-... -

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Basic information

Entry
Database: PDB / ID: 4mm6
TitleCrystal structure of LeuBAT (delta13 mutant) in complex with (S)-duloxetine
ComponentsTransporterTransport protein
KeywordsTRANSPORT PROTEIN / transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / Chem-29E / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, H. / Gouaux, E.
CitationJournal: Nature / Year: 2013
Title: Structural basis for action by diverse antidepressants on biogenic amine transporters.
Authors: Wang, H. / Goehring, A. / Wang, K.H. / Penmatsa, A. / Ressler, R. / Gouaux, E.
History
DepositionSep 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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)58,3324
Polymers57,9881
Non-polymers3433
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.897, 88.383, 81.311
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter / Transport protein


Mass: 57988.266 Da / Num. of mol.: 1
Mutation: N21Y, G24D, I106S, T254S, S256G, A261V, I262L, Y265F, E290S, I359G, P362G, G408T, T409G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf, aq_2077 / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-29E / (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine / Duloxetine / Duloxetine


Mass: 297.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19NOS / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM NaPi, pH7.0, 100 mM NaCl, 32-34% PEG300, 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: Feb 14, 2013
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: 3.1→40 Å / Num. all: 11463 / Num. obs: 10993 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.5 / % possible all: 80.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→38.796 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 529 4.82 %random
Rwork0.2136 ---
obs0.2146 10972 95.14 %-
all-11463 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 23 1 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014163
X-RAY DIFFRACTIONf_angle_d0.9425670
X-RAY DIFFRACTIONf_dihedral_angle_d11.8911413
X-RAY DIFFRACTIONf_chiral_restr0.058632
X-RAY DIFFRACTIONf_plane_restr0.004689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.3940.3421150.2862298X-RAY DIFFRACTION84
3.394-3.88470.25871420.22952681X-RAY DIFFRACTION98
3.8847-4.89280.23651260.19792710X-RAY DIFFRACTION99
4.8928-38.7960.19811460.1992754X-RAY DIFFRACTION99

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