[English] 日本語
Yorodumi
- PDB-1iwg: Crystal structure of Bacterial Multidrug Efflux transporter AcrB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iwg
TitleCrystal structure of Bacterial Multidrug Efflux transporter AcrB
ComponentsAcrBAcriflavine resistance protein family
KeywordsMEMBRANE PROTEIN / Drug resistance / multidrug efflux / transporter / antiporter
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / outer membrane-bounded periplasmic space / membrane / identical protein binding / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsMurakami, S. / Nakashima, R. / Yamashita, E. / Yamaguchi, A.
CitationJournal: NATURE / Year: 2002
Title: Crystal structure of bacterial multidrug efflux transporter AcrB
Authors: Murakami, S. / Nakashima, R. / Yamashita, E. / Yamaguchi, A.
History
DepositionMay 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX determination method: Author determined
Remark 700SHEET determination method: Author determined

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AcrB


Theoretical massNumber of molelcules
Total (without water)114,2181
Polymers114,2181
Non-polymers00
Water0
1
A: AcrB

A: AcrB

A: AcrB


Theoretical massNumber of molelcules
Total (without water)342,6533
Polymers342,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18180 Å2
ΔGint-78 kcal/mol
Surface area112580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.536, 144.536, 519.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein AcrB / Acriflavine resistance protein family / MULTIDRUG EFFLUX PROTEIN


Mass: 114217.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pUC-118 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P31224

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: PEG 2000, Sodium phosphate, sodium citrate, glycerol, dodecyl maltoside, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
128 mg/mlprotein1drop
220 mMsodium phosphate1droppH6.2
310 %glycerol1drop
40.2 %dodecylmaltoside1drop
515-16 %PEG20001reservoir
680 mMsodium phosphate1reservoirpH6.2
720 mMsodium citrate-HCl1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040 / Detector: IMAGE PLATE / Date: Feb 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 198425 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 26406 / Num. measured all: 198425 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 3.5 Å / % possible obs: 98.6 % / Num. unique obs: 2584 / Num. measured obs: 13165 / Rmerge(I) obs: 0.365

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 3.5→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.355 9921 RANDOM
Rwork0.29 --
obs-198425 -
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 0 0 7639
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rfree: 0.355 / Rfactor Rwork: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0032
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg0.867

+
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