[English] 日本語
Yorodumi
- PDB-3b61: EmrE multidrug transporter, apo crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b61
TitleEmrE multidrug transporter, apo crystal form
ComponentsMultidrug transporter emrE
KeywordsMEMBRANE PROTEIN / HELICAL MEMBRANE PROTEIN / MULTIDRUG RESISTANCE TRANSPORTER / SMR / Antiport / Inner membrane / Transmembrane
Function / homology
Function and homology information


EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / glycine betaine transport / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / glycine betaine transport / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity / transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / response to xenobiotic stimulus / DNA damage response / membrane / identical protein binding / plasma membrane
Similarity search - Function
Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein
Similarity search - Domain/homology
Multidrug transporter EmrE
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.5 Å
AuthorsChang, G. / Chen, Y.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: X-ray structure of EmrE supports dual topology model.
Authors: Chen, Y.J. / Pornillos, O. / Lieu, S. / Ma, C. / Chen, A.P. / Chang, G.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multidrug transporter emrE
B: Multidrug transporter emrE
C: Multidrug transporter emrE
D: Multidrug transporter emrE
E: Multidrug transporter emrE
F: Multidrug transporter emrE
G: Multidrug transporter emrE
H: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)95,7068
Polymers95,7068
Non-polymers00
Water0
1
A: Multidrug transporter emrE
B: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Multidrug transporter emrE
D: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Multidrug transporter emrE
F: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Multidrug transporter emrE
H: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.000, 239.200, 284.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

-
Components

#1: Protein
Multidrug transporter emrE / Efflux-multidrug resistance protein emrE / Methyl viologen resistance protein C / Ethidium resistance protein / Coordinate model: Cα atoms only


Mass: 11963.278 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: emrE, eb, mvrC / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23895

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20 mM NaCl, 20 mM sodium acetate, 200-600 mM ammonium sulfate, 15-30% (w/v) PEG-200, and 0.3-0.6% (w/v) NG, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0057, 1.0089, 1.0067
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00571
21.00891
31.00671
ReflectionResolution: 3→50 Å / Num. obs: 13836 / % possible obs: 75.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 12.2
Reflection shellResolution: 4.5→4.66 Å / Num. unique all: 1584 / % possible all: 38.2

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 4.5→19.99 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: The structure contains CA atoms only.
RfactorNum. reflection% reflectionSelection details
Rfree0.362 1369 -RANDOM
Rwork0.318 ---
obs-13836 75.8 %-
Displacement parametersBiso mean: 262.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.06 Å20 Å20 Å2
2---16.89 Å20 Å2
3---10.83 Å2
Refinement stepCycle: LAST / Resolution: 4.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 0 856
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.548 120 -
Rwork0.492 --
obs-1032 38.2 %

+
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