[English] 日本語
Yorodumi
- PDB-6q4o: Fusidic acid bound AcrB_I27A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q4o
TitleFusidic acid bound AcrB_I27A
Components
  • DARPIN
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / Multidrug efflux protein / Membrane protein
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
Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
DECANE / DODECANE / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / (2S)-3-hydroxypropane-1,2-diyl didecanoate / FUSIDIC ACID / HEXANE / N-OCTANE / PHOSPHATIDYLETHANOLAMINE / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTam, H.K. / Pos, K.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB807 (Transport and Communication across Biological Membranes Germany
German Research FoundationDFG EXC115 (Cluster of Excellence Frankfurt Macromolecular Complexes) Germany
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.
Authors: Tam, H.K. / Malviya, V.N. / Foong, W.E. / Herrmann, A. / Malloci, G. / Ruggerone, P. / Vargiu, A.V. / Pos, K.M.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)394,62965
Polymers380,7185
Non-polymers13,91260
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53420 Å2
ΔGint59 kcal/mol
Surface area121420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.203, 162.571, 243.459
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 114694.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 (DE3) / 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) / Gene: artificial gene / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (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 , 11 types, 692 molecules

#4: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical
ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H27NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#9: Chemical ChemComp-FUA / FUSIDIC ACID / Fusidic acid


Mass: 516.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, Antimicrobial*YM
#10: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26
#11: 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
#12: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.05M ADA, PH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.4 Å / Num. obs: 140232 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.193 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 1.363

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMN

5jmn


Resolution: 2.8→47.52 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.873 / SU B: 15.239 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.668 / ESU R Free: 0.333 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25557 6961 5 %RANDOM
Rwork0.21179 ---
obs0.21397 133220 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.537 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å20 Å2
2--2.12 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25988 0 956 643 27587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01327445
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726867
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.65737080
X-RAY DIFFRACTIONr_angle_other_deg1.091.60462291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91253428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59223.1041192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.216154458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.80715123
X-RAY DIFFRACTIONr_chiral_restr0.0430.23675
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0229784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025353
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2274.9313691
X-RAY DIFFRACTIONr_mcbond_other1.2274.9313690
X-RAY DIFFRACTIONr_mcangle_it2.1697.39417108
X-RAY DIFFRACTIONr_mcangle_other2.1697.39417109
X-RAY DIFFRACTIONr_scbond_it1.1575.29713754
X-RAY DIFFRACTIONr_scbond_other1.1575.29713755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0597.81719967
X-RAY DIFFRACTIONr_long_range_B_refined5.70893.731110619
X-RAY DIFFRACTIONr_long_range_B_other5.70893.732110620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 516 -
Rwork0.334 9822 -
obs--99.71 %

+
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