[English] 日本語
Yorodumi
- PDB-3w9i: Structural basis for the inhibition of bacterial multidrug exporters -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w9i
TitleStructural basis for the inhibition of bacterial multidrug exporters
ComponentsMultidrug resistance protein MexB
KeywordsMEMBRANE PROTEIN / MexB / Efflux pump / Transporter / Multidrug efflux pump / MexA / OprM / Inner Membrane / Transport protein
Function / homology
Function and homology information


efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transport / response to antibiotic / 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 resistance protein MexB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsSakurai, K. / Nakashima, R. / Hayashi, K. / Yamaguchi, A.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the inhibition of bacterial multidrug exporters
Authors: Nakashima, R. / Sakurai, K. / Yamasaki, S. / Hayashi, K. / Nagata, C. / Hoshino, K. / Onodera, Y. / Nishino, K. / Yamaguchi, A.
History
DepositionApr 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)685,43322
Polymers677,2636
Non-polymers8,17016
Water1267
1
A: Multidrug resistance protein MexB
B: Multidrug resistance protein MexB
C: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,71611
Polymers338,6313
Non-polymers4,0858
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26790 Å2
ΔGint-98 kcal/mol
Surface area107160 Å2
MethodPISA
2
D: Multidrug resistance protein MexB
E: Multidrug resistance protein MexB
F: Multidrug resistance protein MexB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,71611
Polymers338,6313
Non-polymers4,0858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26140 Å2
ΔGint-99 kcal/mol
Surface area108530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.815, 133.981, 150.467
Angle α, β, γ (deg.)87.14, 69.49, 88.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 1030 / Label seq-ID: 1 - 1030

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DD
12BB
22EE
13CC
23FF

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.612914, 0.665371, 0.426167), (0.665791, 0.144445, 0.732023), (0.425509, 0.732405, -0.53153)-9.6414, 7.20559, 11.39539

-
Components

#1: Protein
Multidrug resistance protein MexB / Multidrug-efflux transporter MexB


Mass: 112877.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: mexB, PA0426 / Plasmid: pUCP20 / Production host: Escherichia coli (E. coli) / Strain (production host): MG1655 / References: UniProt: P52002
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50mM Na Acetate-HCl pH5.0, 300mM NaCl, 25% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 23, 2011
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 241501 / % possible obs: 97.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.753.70.552196.9
2.75-2.83.70.445197.4
2.8-2.853.70.382197.7
2.85-2.913.80.329197.3
2.91-2.973.80.274197.8
2.97-3.043.80.224198.2
3.04-3.123.80.181198.2
3.12-3.23.80.15198.7
3.2-3.33.80.123198.8
3.3-3.43.90.094199
3.4-3.523.90.075199.1
3.52-3.663.90.064199.1
3.66-3.833.90.051199.2
3.83-4.033.80.044199.2
4.03-4.293.80.038199.2
4.29-4.623.80.034199.1
4.62-5.083.80.032198.9
5.08-5.823.90.032199.6
5.82-7.333.90.028199.6
7.33-1003.70.024177.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.35 Å48.33 Å
Translation3.35 Å48.33 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V50

2v50


Resolution: 2.71→48.33 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.3 / SU ML: 0.318 / SU R Cruickshank DPI: 0.8203 / Cross valid method: THROUGHOUT / ESU R: 0.862 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31529 12079 5 %RANDOM
Rwork0.28176 ---
obs0.28346 228777 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20.02 Å20.02 Å2
2--0.06 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46738 0 560 7 47305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01948342
X-RAY DIFFRACTIONr_bond_other_d0.0020.0247367
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.98165669
X-RAY DIFFRACTIONr_angle_other_deg1.1993108907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.87356151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62424.3981860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.059157908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.66315228
X-RAY DIFFRACTIONr_chiral_restr0.3450.27749
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02154173
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210603
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A15395MEDIUM POSITIONAL0.540.5
1A15395MEDIUM THERMAL12.862
2B15608MEDIUM POSITIONAL0.50.5
2B15608MEDIUM THERMAL11.772
3C15607MEDIUM POSITIONAL0.530.5
3C15607MEDIUM THERMAL8.672
LS refinement shellResolution: 2.708→2.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 900 -
Rwork0.392 16271 -
obs--93.29 %

+
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://pdbjlvh1.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