[English] 日本語
Yorodumi
- PDB-2v50: The Missing Part of the Bacterial MexAB-OprM System: Structural d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v50
TitleThe Missing Part of the Bacterial MexAB-OprM System: Structural determination of the Multidrug Exporter MexB
ComponentsMULTIDRUG RESISTANCE PROTEIN MEXB
KeywordsMEMBRANE PROTEIN / MULTIDRUG RESISTANCE PROTEIN / DDM / RND / MEMBRANE / DETERGENT / TRANSPORT / CELL MEMBRANE / TRANSMEMBRANE / CELL INNER MEMBRANE / ANTIBIOTIC RESISTANCE / DRUG-EFFLUX PUMP / TRANSPORT PROTEIN
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
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / 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 PA01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSennhauser, G. / Bukowska, M.A. / Gruetter, M.G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Multidrug Exporter Mexb from Pseudomonas Aeruginosa.
Authors: Sennhauser, G. / Bukowska, M.A. / Briand, C. / Gruetter, M.G.
History
DepositionOct 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
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)686,32114
Polymers682,2366
Non-polymers4,0858
Water00
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)343,1607
Polymers341,1183
Non-polymers2,0424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22450 Å2
ΔGint-99.3 kcal/mol
Surface area109520 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)343,1607
Polymers341,1183
Non-polymers2,0424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22330 Å2
ΔGint-97.8 kcal/mol
Surface area109750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.050, 134.580, 151.020
Angle α, β, γ (deg.)86.99, 69.70, 88.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C AND (RESSEQ 1:1030 )
211CHAIN F AND (RESSEQ 1:1030 )
112CHAIN B AND (RESSEQ 1:668 OR RESSEQ 691:989 OR RESSEQ 996:1030 )
212CHAIN E AND (RESSEQ 1:668 OR RESSEQ 691:989 OR RESSEQ 996:1030 )
113CHAIN A AND (RESSEQ 4:153 OR RESSEQ 165:252 OR RESSEQ...
213CHAIN D AND (RESSEQ 4:153 OR RESSEQ 165:252 OR RESSEQ...

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.6075, 0.6677, 0.4303), (0.6683, 0.1369, 0.7312), (0.4293, 0.7318, -0.5294)32.4441, -35.0499, 38.541
2given(-0.6075, 0.6677, 0.4303), (0.6683, 0.1369, 0.7312), (0.4293, 0.7318, -0.5294)32.4441, -35.0499, 38.541
3given(-0.6064, 0.6678, 0.4317), (0.6679, 0.1331, 0.7323), (0.4315, 0.7324, -0.5267)32.2967, -35.1697, 38.3243

-
Components

#1: Protein
MULTIDRUG RESISTANCE PROTEIN MEXB / MEXB / MULTIDRUG-EFFLUX TRANSPORTER MEXB


Mass: 113706.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PA01 (bacteria) / Plasmid: PET-28 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P52002
#2: 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
Sequence details6 HISTIDINES ADDED AT THE C-TERMINUS FOR PURIFICATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 4.5 / Details: 30% PEG400, 50MM NA-ACETATE, 230MM NACL, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9196
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 176904 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 88.33 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.26
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 87

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8S

2j8s


Resolution: 3→49.76 Å / SU ML: 0.52 / σ(F): 1.99 / Phase error: 34.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 3539 2 %
Rwork0.242 --
obs0.243 176904 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.14 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso mean: 100.94 Å2
Baniso -1Baniso -2Baniso -3
1-6.319 Å223.1156 Å23.664 Å2
2--4.3052 Å213.6682 Å2
3----10.6242 Å2
Refinement stepCycle: LAST / Resolution: 3→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46348 0 280 0 46628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00547576
X-RAY DIFFRACTIONf_angle_d0.96564639
X-RAY DIFFRACTIONf_dihedral_angle_d17.13517144
X-RAY DIFFRACTIONf_chiral_restr0.0667585
X-RAY DIFFRACTIONf_plane_restr0.0048242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C7812X-RAY DIFFRACTIONPOSITIONAL
12F7812X-RAY DIFFRACTIONPOSITIONAL0.016
21B7619X-RAY DIFFRACTIONPOSITIONAL
22E7619X-RAY DIFFRACTIONPOSITIONAL0.019
31A7268X-RAY DIFFRACTIONPOSITIONAL
32D7268X-RAY DIFFRACTIONPOSITIONAL0.024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0044-3.04550.41031240.39266045X-RAY DIFFRACTION84
3.0455-3.0890.45911420.35976978X-RAY DIFFRACTION97
3.089-3.13510.36971440.33747034X-RAY DIFFRACTION97
3.1351-3.18410.37251430.31947012X-RAY DIFFRACTION97
3.1841-3.23630.35031420.31986984X-RAY DIFFRACTION97
3.2363-3.29210.36871460.31197124X-RAY DIFFRACTION97
3.2921-3.3520.33441420.30226981X-RAY DIFFRACTION97
3.352-3.41640.32761410.28786905X-RAY DIFFRACTION97
3.4164-3.48610.34911430.28126999X-RAY DIFFRACTION97
3.4861-3.56190.36281430.28036998X-RAY DIFFRACTION97
3.5619-3.64480.32171430.27467033X-RAY DIFFRACTION97
3.6448-3.73590.29451430.2556983X-RAY DIFFRACTION97
3.7359-3.83680.27721430.24247005X-RAY DIFFRACTION97
3.8368-3.94970.30661420.24216952X-RAY DIFFRACTION97
3.9497-4.07710.26541420.24716995X-RAY DIFFRACTION97
4.0771-4.22280.28781430.24026962X-RAY DIFFRACTION97
4.2228-4.39180.27771410.22746919X-RAY DIFFRACTION96
4.3918-4.59150.23861420.20246946X-RAY DIFFRACTION96
4.5915-4.83340.21091410.19096913X-RAY DIFFRACTION96
4.8334-5.13590.23181420.18146964X-RAY DIFFRACTION97
5.1359-5.5320.22021420.19976979X-RAY DIFFRACTION97
5.532-6.08780.25721420.21456955X-RAY DIFFRACTION97
6.0878-6.96670.2881400.21816874X-RAY DIFFRACTION95
6.9667-8.76950.22731410.18686898X-RAY DIFFRACTION96
8.7695-49.76810.30081420.25266927X-RAY DIFFRACTION96

+
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