[English] 日本語
Yorodumi
- PDB-6vs1: protein C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vs1
Titleprotein C
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN / membrane protein
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / regulation of cellular pH / response to antibiotic / plasma membrane
Similarity search - Function
Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
PRASEODYMIUM ION / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLu, M. / Lu, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094195 United States
CitationJournal: Sci Rep / Year: 2020
Title: Structure and mechanism of a redesigned multidrug transporter from the Major Facilitator Superfamily.
Authors: Wu, H.H. / Symersky, J. / Lu, M.
History
DepositionFeb 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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 MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4573
Polymers41,9231
Non-polymers5332
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.728, 70.405, 112.898
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Multidrug transporter MdfA / Chloramphenicol resistance pump Cmr


Mass: 41923.020 Da / Num. of mol.: 1 / Mutation: E26T/D34M/A150E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mdfA, cmlA, cmr, b0842, JW0826 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY8
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, salts, etc

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 12474 / % possible obs: 97 % / Redundancy: 12 % / CC1/2: 1 / Rsym value: 0.12 / Net I/σ(I): 36
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 300 / CC1/2: 0.43 / Rsym value: 0.7 / % possible all: 91

-
Processing

Software
NameVersionClassification
REFMAC2.1refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→15 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.296 --
Rwork0.28 --
obs0.28 12474 90 %
Displacement parametersBiso max: 398.86 Å2 / Biso mean: 185.9271 Å2 / Biso min: 69.9 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 29 0 2914

+
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