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

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Database: PDB / ID: 4mma
TitleCrystal structure of LeuBAT (delta13 mutant) in complex with clomipramine
ComponentsTransporterTransport protein
KeywordsTRANSPORT PROTEIN / transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / symporter activity / sodium ion transmembrane transport / integral component of plasma membrane / Chem-CXX / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
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.
DepositionSep 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references

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Deposited unit
A: Transporter
hetero molecules

Theoretical massNumber of molelcules
Total (without water)58,3494

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.520, 88.811, 81.225
Angle α, β, γ (deg.)90.00, 94.41, 90.00
Int Tables number5
Space group name H-MC121


#1: Protein Transporter / Transport protein

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-CXX / 3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE / 3-chloro-5-(3-(dimethylamino)propyl)-10,11-dihydro-5H-dibenz[b,f]azepine / Clomipramine

Mass: 314.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23ClN2 / Comment: antidepressant*YM
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.19 %
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

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: 3.3→40 Å / Num. all: 9542 / Num. obs: 8569 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 74.9


ADSCQuantumdata collection
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→38.936 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 36.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 405 4.74 %random
Rwork0.2462 ---
obs0.2469 8538 89.1 %-
all-9542 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→38.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 24 3 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014166
X-RAY DIFFRACTIONf_angle_d0.8715682
X-RAY DIFFRACTIONf_dihedral_angle_d11.8981416
X-RAY DIFFRACTIONf_chiral_restr0.052631
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.77070.33271170.34632404X-RAY DIFFRACTION80
3.7707-4.74940.30241540.26482845X-RAY DIFFRACTION94
4.7494-38.9360.21711340.21012884X-RAY DIFFRACTION93

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