[English] 日本語
Yorodumi
- PDB-9hao: BDM91531 inhibitor bound to the transmembrane domain of AcrB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hao
TitleBDM91531 inhibitor bound to the transmembrane domain of AcrB
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / RND multidrug efflux pump / antimicrobial resistance / allosteric inhibitor / intermediate conformational state
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
TETRADECANE / DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / HEXANE / Chem-LPX / N-OCTANE / : / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMueller, R.T. / Herrmann, A. / Pos, K.M.
Funding support Germany, France, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchBMBF-16GW0236K Germany
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps
Authors: Boernsen, C. / Mueller, R.T. / Pos, K.M.
History
DepositionNov 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
D: DARPIN
E: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,70799
Polymers380,8445
Non-polymers13,86394
Water28,7701597
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55290 Å2
ΔGint18 kcal/mol
Surface area118310 Å2
Unit cell
Length a, b, c (Å)146.184, 161.143, 244.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 5 molecules ABCDE

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114736.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: MG1655 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24a / Details (production host): pET24a_acrB / Production host: Escherichia coli B (bacteria) / Strain (production host): C43(DE3) / Variant (production host): DELTAacrB / References: UniProt: P31224
#2: Protein DARPIN


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE30 / Details (production host): pQE30_110819 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): XL1-Blue

-
Sugars , 1 types, 8 molecules

#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 13 types, 1683 molecules

#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#9: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14
#10: Chemical ChemComp-XE9 / [3-(3-chloranyl-2-piperazin-1-yl-quinolin-6-yl)phenyl]methanamine


Mass: 352.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21ClN4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#12: Chemical ChemComp-DDR / (2S)-3-hydroxypropane-1,2-diyl didecanoate / 1,2-DIDECANOYL-SN-GLYCEROL


Mass: 400.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O5
#13: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#14: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#15: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H44NO7P
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1597 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.45 % / Description: Rod-shaped crystals
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, pH 6.6, 0.19M ammonium sulfate, 9% PEG4000, 5% Glycerol, 0.0025M BDM91531

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 1.94→49.38 Å / Num. obs: 421885 / % possible obs: 99.1 % / Redundancy: 14.1 % / Biso Wilson estimate: 40.34 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.22
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 14.5 % / Num. unique obs: 39235 / CC1/2: 0.406 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→49.38 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 20975 5 %
Rwork0.2021 398299 -
obs0.2033 419274 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.72 Å2
Refinement stepCycle: LAST / Resolution: 1.94→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25888 0 934 1597 28419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427273
X-RAY DIFFRACTIONf_angle_d0.606336819
X-RAY DIFFRACTIONf_chiral_restr0.0424304
X-RAY DIFFRACTIONf_plane_restr0.0054611
X-RAY DIFFRACTIONf_dihedral_angle_d14.20159951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.39045990.37511497X-RAY DIFFRACTION86.41
1.96-1.990.35846650.366612692X-RAY DIFFRACTION95.67
1.99-2.010.35886920.332613075X-RAY DIFFRACTION98.11
2.01-2.030.33166980.318613148X-RAY DIFFRACTION98.76
2.03-2.060.32076960.29313179X-RAY DIFFRACTION99.24
2.06-2.090.30096980.281913227X-RAY DIFFRACTION99.42
2.09-2.120.31876970.271713227X-RAY DIFFRACTION99.49
2.12-2.150.27297000.256513303X-RAY DIFFRACTION99.56
2.15-2.180.28546980.253913215X-RAY DIFFRACTION99.63
2.18-2.220.27826970.246213262X-RAY DIFFRACTION99.63
2.22-2.260.28717010.246513282X-RAY DIFFRACTION99.72
2.26-2.30.2577000.235913297X-RAY DIFFRACTION99.7
2.3-2.340.25617020.227713272X-RAY DIFFRACTION99.76
2.34-2.390.25127000.220413315X-RAY DIFFRACTION99.74
2.39-2.440.24037010.212913319X-RAY DIFFRACTION99.64
2.44-2.50.25097020.207913304X-RAY DIFFRACTION99.84
2.5-2.560.24017010.207513368X-RAY DIFFRACTION99.84
2.56-2.630.2357000.20113300X-RAY DIFFRACTION99.85
2.63-2.710.23967050.204813370X-RAY DIFFRACTION99.89
2.71-2.80.23657010.209113348X-RAY DIFFRACTION99.97
2.8-2.90.23747060.201113395X-RAY DIFFRACTION99.93
2.9-3.010.22437050.197113403X-RAY DIFFRACTION99.97
3.01-3.150.21837080.196313429X-RAY DIFFRACTION99.98
3.15-3.320.22367060.198313422X-RAY DIFFRACTION99.99
3.32-3.520.20887080.186713449X-RAY DIFFRACTION99.96
3.52-3.80.20377080.180313482X-RAY DIFFRACTION100
3.8-4.180.20037130.18113536X-RAY DIFFRACTION100
4.18-4.780.17737120.165913536X-RAY DIFFRACTION100
4.78-6.020.20747200.179913662X-RAY DIFFRACTION99.99
6.02-49.380.21267360.202213985X-RAY DIFFRACTION99.45

+
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