[English] 日本語
Yorodumi
- PDB-7akz: Deciphering the role of the channel constrictions in the opening ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7akz
TitleDeciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM efflux pump from Pseudomonas aeruginosa
ComponentsOuter membrane protein OprM
KeywordsTRANSLOCASE / Efflux pump / Antibiotic resistance / TolC-like / Channel.
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / response to antibiotic / membrane
Similarity search - Function
RND efflux system, outer membrane lipoprotein, NodT / : / Outer membrane efflux protein / Outer membrane efflux protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PALMITIC ACID / Outer membrane protein OprM
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNtsogo Enguene, V.Y. / Monlezun, L. / Ma, M. / Garnier, C. / Lascombe, M.B. / Salem, M. / Guenard, S. / Plesiat, P. / Llanes, C. / Phan, G. / Broutin, I.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: To Be Published
Title: Deciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM efflux pump from Pseudomonas aeruginosa
Authors: Ntsogo Enguene, V.Y. / Monlezun, L. / Ma, M. / Garnier, C. / Lascombe, M.B. / Salem, M. / Guenard, S. / Plesiat, P. / Llanes, C. / Phan, G. / Broutin, I.
History
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein OprM
B: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1166
Polymers102,9832
Non-polymers1,1344
Water00
1
A: Outer membrane protein OprM
hetero molecules

A: Outer membrane protein OprM
hetero molecules

A: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,87515
Polymers154,4743
Non-polymers3,40112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18890 Å2
ΔGint-66 kcal/mol
Surface area61240 Å2
MethodPISA
2
B: Outer membrane protein OprM

B: Outer membrane protein OprM

B: Outer membrane protein OprM


Theoretical massNumber of molelcules
Total (without water)154,4743
Polymers154,4743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area15500 Å2
ΔGint-92 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.059, 86.059, 1049.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Outer membrane protein OprM


Mass: 51491.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: oprM, oprK, PA0427 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51487
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 400, sodium citrate, sodium chloride, magnesium chloride.

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 195912 / % possible obs: 98.1 % / Redundancy: 6.97 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 7.59
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 1.71 / Num. unique obs: 11999

-
Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5K

3d5k


Resolution: 3.2→49.99 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3184 1275 4.99 %
Rwork0.2705 24288 -
obs0.2729 25563 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.51 Å2 / Biso mean: 96.5424 Å2 / Biso min: 36.32 Å2
Refinement stepCycle: final / Resolution: 3.2→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 65 0 7005
Biso mean--81.36 --
Num. residues----908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.330.40411310.37226692800100
3.33-3.480.36931290.330326642793100
3.48-3.660.38671450.293126552800100
3.66-3.890.33991360.269827142850100
3.89-4.190.30121270.26122680280799
4.19-4.610.29091390.24062687282699
4.61-5.280.2951430.2242716285999
5.28-6.650.30721710.27672696286798
6.65-49.990.30781540.27152807296195

+
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