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- PDB-4mm9: Crystal structure of LeuBAT (delta13 mutant) in complex with fluv... -

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Basic information

Entry
Database: PDB / ID: 4mm9
TitleCrystal structure of LeuBAT (delta13 mutant) in complex with fluvoxamine
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 / Fluvoxamine / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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_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.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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3534
Polymers57,9881
Non-polymers3643
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)90.810, 88.070, 81.500
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter


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-FVX / Fluvoxamine / 2-[({(1E)-5-methoxy-1-[4-(trifluoromethyl)phenyl]pentylidene}amino)oxy]ethanamine


Mass: 318.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21F3N2O2 / Comment: antidepressant, inhibitor*YM
#4: Water ChemComp-HOH / 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: 2.8 Å3/Da / Density % sol: 56.08 %
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: 2.9→51.3 Å / Num. all: 14312 / Num. obs: 14298 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.2
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.248 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 36.12 / Stereochemistry target values: ML
Details: THE HIGH REAL SPACE R FOR THE LIGAND (FVX), IS DUE TO THE WEAK DENSITY OF TWO ALKYL CHAINS OF THE LIGAND (THE DENSITY FOR THE PHENYL GROUP IS VERY STRONG). THE AUTHORS MODELED THE LIGAND ...Details: THE HIGH REAL SPACE R FOR THE LIGAND (FVX), IS DUE TO THE WEAK DENSITY OF TWO ALKYL CHAINS OF THE LIGAND (THE DENSITY FOR THE PHENYL GROUP IS VERY STRONG). THE AUTHORS MODELED THE LIGAND POSITION BASED ON BOTH FO-FC AND 2FO-FC MAP. ALSO THE CURRENT POSITION AGREES WITH THE CHEMISTRY AND OTHER DRUGS POSITION THE AUTHORS DEPOSITED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 710 5.02 %random
Rwork0.2304 ---
obs0.2324 14148 98.92 %-
all-14312 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 24 1 3989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094121
X-RAY DIFFRACTIONf_angle_d0.7815614
X-RAY DIFFRACTIONf_dihedral_angle_d12.2371410
X-RAY DIFFRACTIONf_chiral_restr0.053624
X-RAY DIFFRACTIONf_plane_restr0.004680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.1240.40771460.35872642X-RAY DIFFRACTION98
3.124-3.43830.36131560.28752629X-RAY DIFFRACTION98
3.4383-3.93560.27621530.22022674X-RAY DIFFRACTION99
3.9356-4.95740.23641250.20622723X-RAY DIFFRACTION100
4.9574-45.2480.23731300.21282770X-RAY DIFFRACTION100

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