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- PDB-4mmf: Crystal structure of LeuBAT (delta5 mutant) in complex with mazindol -

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Basic information

Entry
Database: PDB / ID: 4mmf
TitleCrystal structure of LeuBAT (delta5 mutant) in complex with mazindol
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-29Q / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)117,97813
Polymers115,8542
Non-polymers2,12311
Water93752
1
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8436
Polymers57,9271
Non-polymers9155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1357
Polymers57,9271
Non-polymers1,2086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-36 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.227, 92.137, 87.827
Angle α, β, γ (deg.)90.00, 93.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transporter / Transport protein


Mass: 57927.195 Da / Num. of mol.: 2 / Mutation: N21Y, G24D, T254S, S256G, 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 58.1 %
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: 2.7→40 Å / Num. all: 37303 / Num. obs: 37117 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.4 / % possible all: 95.8

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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: 2.7→38.85 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1854 5 %
Rwork0.199 --
obs0.201 37062 99.1 %
all-37303 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8024 0 144 52 8220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088446
X-RAY DIFFRACTIONf_angle_d1.1311519
X-RAY DIFFRACTIONf_dihedral_angle_d16.162993
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 (%)
2.7-2.76260.31941260.2572466X-RAY DIFFRACTION90
2.7626-2.84390.28031250.22652727X-RAY DIFFRACTION100
2.8439-2.93570.25691450.21582710X-RAY DIFFRACTION100
2.9357-3.04060.27441530.21722710X-RAY DIFFRACTION100
3.0406-3.16220.2881540.21242690X-RAY DIFFRACTION100
3.1622-3.30610.28521420.20092722X-RAY DIFFRACTION100
3.3061-3.48030.25751620.19842719X-RAY DIFFRACTION100
3.4803-3.69820.22181320.19022729X-RAY DIFFRACTION100
3.6982-3.98350.2231460.19962724X-RAY DIFFRACTION100
3.9835-4.38380.18841260.18792750X-RAY DIFFRACTION100
4.3838-5.0170.24191440.17152729X-RAY DIFFRACTION100
5.017-6.31660.23661550.212735X-RAY DIFFRACTION100
6.3166-38.85120.2061440.19792797X-RAY DIFFRACTION99

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