[English] 日本語
Yorodumi
- PDB-3gww: Leucine transporter LeuT in complex with S-fluoxetine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gww
TitleLeucine transporter LeuT in complex with S-fluoxetine
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / NEUROTRANSMITTER / TRANSMEMBRANE TRANSPORT / INTEGRAL MEMBRANE PROTEIN / ANTIDEPRESSANT / NSS / Symport / Transmembrane / Transport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / LEUCINE / Chem-SFX / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsZhou, Z. / Zhen, J. / Karpowich, N.K. / Law, C.J. / Reith, M.E.A. / Wang, D.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Antidepressant specificity of serotonin transporter suggested by three LeuT-SSRI structures.
Authors: Zhou, Z. / Zhen, J. / Karpowich, N.K. / Law, C.J. / Reith, M.E. / Wang, D.N.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0975
Polymers57,6111
Non-polymers4864
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,19510
Polymers115,2222
Non-polymers9738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2880 Å2
ΔGint-33 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.353, 86.284, 80.624
Angle α, β, γ (deg.)90.000, 95.160, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Transporter


Mass: 57610.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_2077, LeuT, snf / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / 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-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-SFX / (3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine / Fluoxetine


Mass: 309.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18F3NO / Comment: antidepressant, inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG550 MME, NACL, pH 7, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.46→27.28 Å / Num. obs: 19665 / % possible obs: 90.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.444 / Net I/σ(I): 24.024
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.46-2.552.60.18611700.831153.8
2.55-2.652.70.18515430.864172.5
2.65-2.7730.16619190.799188.8
2.77-2.923.40.15621210.817197.2
2.92-3.13.80.13621230.968198.6
3.1-3.343.80.09921381.112198.9
3.34-3.673.80.07621511.51198.9
3.67-4.213.70.0621362199.2
4.21-5.33.70.04921732.294199.3
5.3-503.60.0421912.235197.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2.46→27.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.95 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 993 5.1 %RANDOM
Rwork0.204 ---
obs0.205 19565 91.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.49 Å2 / Biso mean: 47.054 Å2 / Biso min: 24.45 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å2-2.15 Å2
2--0.05 Å20 Å2
3----3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.46→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 33 23 4047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224156
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.9535646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.175499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55321.988161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06215644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1271520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023093
X-RAY DIFFRACTIONr_nbd_refined0.1830.22024
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0330.21
X-RAY DIFFRACTIONr_mcbond_it0.3711.52492
X-RAY DIFFRACTIONr_mcangle_it0.68224007
X-RAY DIFFRACTIONr_scbond_it0.60131762
X-RAY DIFFRACTIONr_scangle_it1.0244.51639
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 49 -
Rwork0.244 791 -
all-840 -
obs--53.03 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more