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- PDB-1lnw: CRYSTAL STRUCTURE OF THE MEXR REPRESSOR OF THE MEXAB-OPRM MULTIDR... -

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Basic information

Entry
Database: PDB / ID: 1lnw
TitleCRYSTAL STRUCTURE OF THE MEXR REPRESSOR OF THE MEXAB-OPRM MULTIDRUG EFFLUX OPERON OF PSEUDOMONAS AERUGINOSA
ComponentsMultidrug resistance operon repressor
KeywordsTRANSCRIPTION REPRESSOR / MexR / repressor / DNA binding protein / regulator of mexRAB-oprM operon
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 / MAD / Resolution: 2.1 Å
AuthorsLim, D.C. / Poole, K. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the MexR repressor of the mexRAB-oprM multidrug efflux operon of Pseudomonas aeruginosa.
Authors: Lim, D. / Poole, K. / Strynadka, N.C.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
C: Multidrug resistance operon repressor
D: Multidrug resistance operon repressor
E: Multidrug resistance operon repressor
F: Multidrug resistance operon repressor
G: Multidrug resistance operon repressor
H: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)137,7768
Polymers137,7768
Non-polymers00
Water3,855214
1
A: Multidrug resistance operon repressor
B: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)34,4442
Polymers34,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-48 kcal/mol
Surface area15480 Å2
MethodPISA
2
C: Multidrug resistance operon repressor
D: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)34,4442
Polymers34,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-47 kcal/mol
Surface area15560 Å2
MethodPISA
3
E: Multidrug resistance operon repressor
F: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)34,4442
Polymers34,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-49 kcal/mol
Surface area14470 Å2
MethodPISA
4
G: Multidrug resistance operon repressor
H: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)34,4442
Polymers34,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-49 kcal/mol
Surface area14890 Å2
MethodPISA
5
G: Multidrug resistance operon repressor
H: Multidrug resistance operon repressor

A: Multidrug resistance operon repressor
B: Multidrug resistance operon repressor
C: Multidrug resistance operon repressor
D: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)103,3326
Polymers103,3326
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
identity operation1_555x,y,z1
Buried area20620 Å2
ΔGint-161 kcal/mol
Surface area39020 Å2
MethodPISA
6
A: Multidrug resistance operon repressor
B: Multidrug resistance operon repressor

G: Multidrug resistance operon repressor
H: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)68,8884
Polymers68,8884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area12230 Å2
ΔGint-105 kcal/mol
Surface area27440 Å2
MethodPISA
7
A: Multidrug resistance operon repressor
B: Multidrug resistance operon repressor
C: Multidrug resistance operon repressor
D: Multidrug resistance operon repressor


Theoretical massNumber of molelcules
Total (without water)68,8884
Polymers68,8884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-104 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.910, 72.654, 240.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. There are four dimers in the asymmetric units, consisting of chain A with B, chain C with D, chain E with F and chain G with H.

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Components

#1: Protein
Multidrug resistance operon repressor / MexR


Mass: 17222.027 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamdaDE3 / References: UniProt: P52003
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CaCl2, NaCl, NaAcetate, MES, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18.8 mg/mlprotein1drop
210 mMTCEP1drop
320 mM1reservoirCaCl2
465 mM1reservoirNaCl
56 mMMES1reservoirpH6.
64 mMsodium acetate1reservoirpH5.
710 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2001
RadiationMonochromator: silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 63205 / Num. obs: 63175 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 30.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4154 / Rsym value: 0.34 / % possible all: 60.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 63205 / Num. measured all: 352292 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 60.5 % / Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→25.03 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 3190 5 %RANDOM
Rwork0.242 ---
all0.2446 63205 --
obs0.242 63175 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9569 Å2 / ksol: 0.337589 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2--2.89 Å20 Å2
3----5.26 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 0 214 9130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 386 5.5 %
Rwork0.27 6677 -
obs--61 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.2446 / Rfactor obs: 0.242 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.347 / Rfactor Rwork: 0.27

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