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- PDB-4zzl: MexR R21W derepressor mutant causing multidrug resistance in P. a... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

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

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Sample preparation

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

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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

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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 %

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