[English] 日本語
Yorodumi
- PDB-21fp: Chloramphenicol-bound MexB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 21fp
TitleChloramphenicol-bound MexB
ComponentsMultidrug resistance protein MexB
KeywordsMEMBRANE PROTEIN / Drug efflux / RND transporter
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transport / response to antibiotic / 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
CHLORAMPHENICOL / Multidrug resistance protein MexB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsUeda, Y. / Yonehara, R. / Nakagawa, A. / Yamashita, E.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K23822 Japan
Japan Society for the Promotion of Science (JSPS)21K19337 Japan
CitationJournal: J.Biochem. / Year: 2026
Title: Structure of chloramphenicol-bound MexB reveals residues in the distal binding pocket that are critical for substrate recognition.
Authors: Ueda, Y. / Yonehara, R. / Ishizaka-Ikeda, E. / Nakagawa, A. / Yamashita, E.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,1684
Polymers341,8453
Non-polymers3231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19540 Å2
ΔGint-95 kcal/mol
Surface area110960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.874, 169.173, 171.926
Angle α, β, γ (deg.)90.000, 102.156, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

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


Mass: 113948.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexB, PA0426 / Production host: Escherichia coli (E. coli) / References: UniProt: P52002
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH8.0, 0.2 M KCl, 8% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.89→51.02 Å / Num. obs: 126964 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 102.19 Å2 / CC1/2: 0.991 / Net I/σ(I): 10.3
Reflection shellResolution: 2.89→2.92 Å / Num. unique obs: 3801 / CC1/2: 0.353

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→51.02 Å / SU ML: 0.5297 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2798 6460 5.09 %
Rwork0.2235 120504 -
obs0.2264 126964 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.73 Å2
Refinement stepCycle: LAST / Resolution: 2.89→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23388 0 20 0 23408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009423883
X-RAY DIFFRACTIONf_angle_d1.165232458
X-RAY DIFFRACTIONf_chiral_restr0.05653788
X-RAY DIFFRACTIONf_plane_restr0.00894166
X-RAY DIFFRACTIONf_dihedral_angle_d19.22218630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.920.45462060.4683595X-RAY DIFFRACTION89.5
2.92-2.960.4591960.41423735X-RAY DIFFRACTION93.02
2.96-2.990.40271940.40063926X-RAY DIFFRACTION97.98
2.99-3.030.40812320.38264038X-RAY DIFFRACTION99.14
3.03-3.070.41432050.38664003X-RAY DIFFRACTION99.39
3.07-3.110.42132060.35674041X-RAY DIFFRACTION99.62
3.11-3.160.40422430.32754004X-RAY DIFFRACTION99.6
3.16-3.20.37022270.31923975X-RAY DIFFRACTION99.81
3.2-3.250.35192160.29574081X-RAY DIFFRACTION99.86
3.25-3.310.38372440.2934005X-RAY DIFFRACTION99.91
3.31-3.360.36341790.29284023X-RAY DIFFRACTION99.95
3.36-3.430.32692180.29394052X-RAY DIFFRACTION99.7
3.43-3.490.32572370.29574023X-RAY DIFFRACTION99.86
3.49-3.560.38212190.25594019X-RAY DIFFRACTION99.88
3.56-3.640.34742230.24594019X-RAY DIFFRACTION99.98
3.64-3.730.3322160.23844052X-RAY DIFFRACTION99.91
3.73-3.820.30972150.22224031X-RAY DIFFRACTION99.86
3.82-3.920.29852170.21644081X-RAY DIFFRACTION99.91
3.92-4.040.27662070.21794065X-RAY DIFFRACTION99.98
4.04-4.170.27692100.21824031X-RAY DIFFRACTION99.95
4.17-4.320.30812030.21764057X-RAY DIFFRACTION99.95
4.32-4.490.25472130.20634032X-RAY DIFFRACTION100
4.49-4.690.25872310.19634035X-RAY DIFFRACTION99.93
4.69-4.940.27632230.19714071X-RAY DIFFRACTION100
4.94-5.250.25952050.20664070X-RAY DIFFRACTION99.98
5.25-5.650.27732030.21714067X-RAY DIFFRACTION99.98
5.65-6.220.28012330.22154074X-RAY DIFFRACTION100
6.22-7.120.26172000.2064091X-RAY DIFFRACTION99.98
7.12-8.960.19942240.16144080X-RAY DIFFRACTION100
8.96-51.020.21932150.19464128X-RAY DIFFRACTION99.06

+
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