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- PDB-4mmd: Crystal structure of LeuBAT (delta6 mutant) in complex with (S)-d... -

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Basic information

Entry
Database: PDB / ID: 4mmd
TitleCrystal structure of LeuBAT (delta6 mutant) in complex with (S)-duloxetine
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / Chem-29E / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Apr 15, 2020Group: Database references / Structure summary / Category: chem_comp / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)117,70111
Polymers116,1372
Non-polymers1,5649
Water2,144119
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2897
Polymers58,0681
Non-polymers1,2216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4124
Polymers58,0681
Non-polymers3433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-49 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.409, 92.207, 88.308
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transporter


Mass: 58068.391 Da / Num. of mol.: 2 / Mutation: N21Y, G24D, T254S, S256G, Y265F, I359G
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-29E / (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine / Duloxetine


Mass: 297.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19NOS / Comment: medication, inhibitor*YM
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 100 mM glycine (pH9.4), 0.1 M Li2SO4, 29%-31% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 60030 / Num. obs: 59970 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.4
Reflection shellResolution: 2.3→2.38 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.984 Å / SU ML: 0.29 / σ(F): 1.33 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 3026 5.05 %random
Rwork0.2128 ---
obs0.2144 59868 99.58 %-
all-60030 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→35.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8022 0 106 119 8247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048382
X-RAY DIFFRACTIONf_angle_d1.03111405
X-RAY DIFFRACTIONf_dihedral_angle_d15.0182929
X-RAY DIFFRACTIONf_chiral_restr0.0341266
X-RAY DIFFRACTIONf_plane_restr0.0051382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33550.3561980.29092502X-RAY DIFFRACTION96
2.3355-2.37380.34521450.26662595X-RAY DIFFRACTION100
2.3738-2.41470.32151460.27752544X-RAY DIFFRACTION100
2.4147-2.45860.3081360.27562550X-RAY DIFFRACTION99
2.4586-2.50590.34831260.25882576X-RAY DIFFRACTION100
2.5059-2.5570.30931460.23972597X-RAY DIFFRACTION100
2.557-2.61260.26011380.23972575X-RAY DIFFRACTION100
2.6126-2.67340.25891290.21862567X-RAY DIFFRACTION100
2.6734-2.74020.30491310.20642584X-RAY DIFFRACTION100
2.7402-2.81430.23941470.19322588X-RAY DIFFRACTION100
2.8143-2.8970.24071340.19892588X-RAY DIFFRACTION100
2.897-2.99050.27591490.19762570X-RAY DIFFRACTION100
2.9905-3.09730.25041350.19712592X-RAY DIFFRACTION100
3.0973-3.22130.24021350.20422578X-RAY DIFFRACTION100
3.2213-3.36780.2331460.20242600X-RAY DIFFRACTION100
3.3678-3.54520.19271390.20192613X-RAY DIFFRACTION100
3.5452-3.76710.24771300.19562572X-RAY DIFFRACTION100
3.7671-4.05760.24171400.20912591X-RAY DIFFRACTION100
4.0576-4.46520.18631460.21152593X-RAY DIFFRACTION100
4.4652-5.10980.24581320.19272612X-RAY DIFFRACTION100
5.1098-6.43180.2411550.23442607X-RAY DIFFRACTION100
6.4318-35.98810.23971430.20922648X-RAY DIFFRACTION99

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