[English] 日本語
Yorodumi
- PDB-4lz9: Structure of MATE multidrug transporter DinF-BH in complex with R6G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lz9
TitleStructure of MATE multidrug transporter DinF-BH in complex with R6G
ComponentsBH2163 protein
KeywordsTRANSPORT PROTEIN / multidrug transporter
Function / homology
Function and homology information


antiporter activity / xenobiotic transmembrane transporter activity / response to antibiotic / plasma membrane
Similarity search - Function
Multidrug and toxic compound extrusion MepA-like / : / : / Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
RHODAMINE 6G / Multidrug export protein MepA
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.7 Å
AuthorsLu, M. / Radchenko, M. / Symersky, J. / Nie, R. / Guo, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural insights into H(+)-coupled multidrug extrusion by a MATE transporter
Authors: Lu, M. / Radchenko, M. / Symersky, J. / Nie, R. / Guo, Y.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: BH2163 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0592
Polymers48,6151
Non-polymers4441
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.181, 93.887, 102.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein BH2163 protein / Coordinate model: Cα atoms only


Mass: 48615.172 Da / Num. of mol.: 1 / Fragment: UNP residues 3-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KAX3
#2: Chemical ChemComp-RHQ / RHODAMINE 6G


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N2O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→60 Å / Num. all: 9715 / Num. obs: 9220 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.066
Reflection shellHighest resolution: 3.7 Å / % possible all: 95

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.7→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: The coordinates contain only a CA trace.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 440 -Random
Rwork0.29 ---
obs0.3 8797 95 %-
all-9350 --
Refinement stepCycle: LAST / Resolution: 3.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 33 0 479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg2
X-RAY DIFFRACTIONr_bond_refined_d0.011

+
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