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- PDB-4mme: Crystal structure of LeuBAT (delta6 mutant) in complex with mazindol -

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Basic information

Entry
Database: PDB / ID: 4mme
TitleCrystal structure of LeuBAT (delta6 mutant) in complex with mazindol
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-29Q / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / 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_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 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

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Assembly

Deposited unit
A: Transporter
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,26013
Polymers116,1372
Non-polymers2,12311
Water2,738152
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2767
Polymers58,0681
Non-polymers1,2086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9846
Polymers58,0681
Non-polymers9155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-38 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.258, 92.825, 87.530
Angle α, β, γ (deg.)90.00, 93.75, 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-29Q / (5R)-5-(4-chlorophenyl)-2,5-dihydro-3H-imidazo[2,1-a]isoindol-5-ol


Mass: 284.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13ClN2O
#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.: 5
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.: 152 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
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: 2.5→50 Å / Num. all: 46645 / Num. obs: 46598 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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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: 2.5→40.985 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
Details: THE HIGH REAL SPACE R FOR TWO BOG MOLECULES IS DUE TO WEAK ELECTRON DENSITIES FOR THE MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2352 5.06 %random
Rwork0.2044 ---
obs0.2058 46520 99.53 %-
all-46645 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→40.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8022 0 144 152 8318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098444
X-RAY DIFFRACTIONf_angle_d1.12811515
X-RAY DIFFRACTIONf_dihedral_angle_d13.312991
X-RAY DIFFRACTIONf_chiral_restr0.0611266
X-RAY DIFFRACTIONf_plane_restr0.0051382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54960.32851140.26132491X-RAY DIFFRACTION95
2.5496-2.60510.29221330.23932571X-RAY DIFFRACTION100
2.6051-2.66570.2561540.232568X-RAY DIFFRACTION100
2.6657-2.73230.28131470.22172609X-RAY DIFFRACTION100
2.7323-2.80620.26471290.20692599X-RAY DIFFRACTION100
2.8062-2.88870.26831420.20272575X-RAY DIFFRACTION100
2.8887-2.98190.23191320.19462597X-RAY DIFFRACTION100
2.9819-3.08850.22941380.19572618X-RAY DIFFRACTION100
3.0885-3.21210.23371500.1982578X-RAY DIFFRACTION100
3.2121-3.35820.24161260.19462625X-RAY DIFFRACTION100
3.3582-3.53520.22261540.19992583X-RAY DIFFRACTION100
3.5352-3.75650.25161430.18562590X-RAY DIFFRACTION100
3.7565-4.04630.22221350.2022633X-RAY DIFFRACTION100
4.0463-4.45310.22491570.2032596X-RAY DIFFRACTION100
4.4531-5.09640.22661190.19132631X-RAY DIFFRACTION100
5.0964-6.4170.22791470.22592623X-RAY DIFFRACTION100
6.417-40.99080.2061320.20492681X-RAY DIFFRACTION99

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