[English] 日本語
Yorodumi
- PDB-4zzl: MexR R21W derepressor mutant causing multidrug resistance in P. a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zzl
TitleMexR R21W derepressor mutant causing multidrug resistance in P. aeruginosa by mexAB-oprM efflux pump expression
ComponentsMULTIDRUG RESISTANCE OPERON REPRESSOR
KeywordsTRANSCRIPTION / MEXR / MEXAB-OPRM EFFLUX PUMP / MD SIMULATION
Function / homology
Function and homology information


negative regulation of transmembrane transport / DNA-binding transcription repressor activity / negative regulation of protein secretion / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Multidrug resistance operon repressor
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAnandapadamanaban, M. / Pilstal, R. / Ziauddin, J.M.E. / Moche, M. / Wallner, B. / Sunnerhagen, M.
CitationJournal: Structure / Year: 2016
Title: Mutation-Induced Population Shift in the Mexr Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for Marr Family Derepression.
Authors: Anandapadamanaban, M. / Pilstal, R. / Andresen, C. / Trewhella, J. / Moche, M. / Wallner, B. / Sunnerhagen, M.
History
DepositionApr 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MULTIDRUG RESISTANCE OPERON REPRESSOR
B: MULTIDRUG RESISTANCE OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9104
Polymers36,7262
Non-polymers1842
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-54.2 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.880, 84.880, 114.187
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein MULTIDRUG RESISTANCE OPERON REPRESSOR / MEXR


Mass: 18363.008 Da / Num. of mol.: 2 / Fragment: HTH MARR-TYPE, RESIDUES 5-139 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PNIC28-BSA4 VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: P52003
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOUR CONSTRUCT STARTS FROM VAL 5 IN THE UNIPROT SEQUENCE, EXTRA SEQUENCE IN N-TERMINAL ...OUR CONSTRUCT STARTS FROM VAL 5 IN THE UNIPROT SEQUENCE, EXTRA SEQUENCE IN N-TERMINAL (MHHHHHHSSGVDLGTENLYFQSM)IS TEV PROTEASE CLEAVABLE 6X-HIS TAG, AND ITS LEFT UNCLEAVED PRIOR TO CRYSTALLIZATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.96 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.19→57.09 Å / Num. obs: 24956 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Biso Wilson estimate: 45.09 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.9
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 4.7 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNW

1lnw


Resolution: 2.19→45.09 Å / Cor.coef. Fo:Fc: 0.9445 / Cor.coef. Fo:Fc free: 0.9391 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.142 / SU Rfree Cruickshank DPI: 0.141
Details: RESIDUES 30-32 ARE DISORDERED DEPOSITED MODEL SIDE-CHAINS FOR THE FOLLOWING RESIDUES ARE REMOVED DUE TO LACK OF ELECTRON DENSITY MAP. CHAIN A, ASP29, ASP34, ASP64, ASP99 AND CHAINB LEU139
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1268 5.09 %RANDOM
Rwork0.1913 ---
obs0.192 24921 99.62 %-
Displacement parametersBiso mean: 52.69 Å2
Baniso -1Baniso -2Baniso -3
1--5.4456 Å20 Å20 Å2
2---5.4456 Å20 Å2
3---10.8912 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.19→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 12 126 2398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012349HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983182HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1139SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes337HARMONIC5
X-RAY DIFFRACTIONt_it2349HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion300SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2864SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.28 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2696 135 5.11 %
Rwork0.2173 2505 -
all0.22 2640 -
obs--99.62 %

+
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