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- PDB-4mm4: Crystal structure of LeuBAT (delta13 mutant) in complex with paro... -

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Basic information

Entry
Database: PDB / ID: 4mm4
TitleCrystal structure of LeuBAT (delta13 mutant) in complex with paroxetine
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / LeuT fold / transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / Paroxetine / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.886 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 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7639
Polymers115,9772
Non-polymers7867
Water543
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3644
Polymers57,9881
Non-polymers3753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3995
Polymers57,9881
Non-polymers4114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-70 kcal/mol
Surface area36860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.424, 92.085, 84.772
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transporter


Mass: 57988.266 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine


Mass: 329.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20FNO3 / Comment: medication, antidepressant, inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.4
Details: 100 mM glycine (pH9.4), 0.1M Li2SO4, 29%-31% PEG400, VAPOR DIFFUSION, 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: 2.886→40 Å / Num. all: 30590 / Num. obs: 30223 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 11
Reflection shellResolution: 2.886→3 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.886→37.313 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1515 5.03 %random
Rwork0.2193 ---
obs0.2205 30104 98.17 %-
all-30590 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.886→37.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7909 0 53 3 7965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118231
X-RAY DIFFRACTIONf_angle_d0.82711220
X-RAY DIFFRACTIONf_dihedral_angle_d11.8232805
X-RAY DIFFRACTIONf_chiral_restr0.0291247
X-RAY DIFFRACTIONf_plane_restr0.0041359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.886-2.97910.36321350.31682396X-RAY DIFFRACTION91
2.9791-3.08550.26631200.29022547X-RAY DIFFRACTION97
3.0855-3.2090.31041330.26362615X-RAY DIFFRACTION99
3.209-3.3550.25321440.24122610X-RAY DIFFRACTION99
3.355-3.53170.29731350.22972631X-RAY DIFFRACTION99
3.5317-3.75280.24671300.21662603X-RAY DIFFRACTION99
3.7528-4.04220.2291450.2142635X-RAY DIFFRACTION99
4.0422-4.44840.22131510.20042592X-RAY DIFFRACTION100
4.4484-5.09070.21731370.19012652X-RAY DIFFRACTION100
5.0907-6.40850.23491430.22282647X-RAY DIFFRACTION100
6.4085-37.3130.21541420.19872661X-RAY DIFFRACTION98

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