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- PDB-1jbg: Crystal Structure of MtaN, the Bacillus subtilis Multidrug Transp... -

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Basic information

Entry
Database: PDB / ID: 1jbg
TitleCrystal Structure of MtaN, the Bacillus subtilis Multidrug Transporter Activator, N-terminus
Componentstranscription activator of multidrug-efflux transporter genes mta
KeywordsTRANSCRIPTION / winged helix-turn-helix / antiparallel coiled-coil
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR, DNA binding / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance ...TipA-like multidrug resistance regulator, antibiotic-recognition domain / TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / MerR, DNA binding / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional activator mta
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsGodsey, M.H. / Neyfakh, A.A. / Brennan, R.G.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of MtaN, a global multidrug transporter gene activator.
Authors: Godsey, M.H. / Baranova, N.N. / Neyfakh, A.A. / Brennan, R.G.
History
DepositionJun 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcription activator of multidrug-efflux transporter genes mta


Theoretical massNumber of molelcules
Total (without water)12,8621
Polymers12,8621
Non-polymers00
Water28816
1
A: transcription activator of multidrug-efflux transporter genes mta

A: transcription activator of multidrug-efflux transporter genes mta


Theoretical massNumber of molelcules
Total (without water)25,7242
Polymers25,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+3/2,z1
Buried area2060 Å2
ΔGint-26 kcal/mol
Surface area13540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.382, 67.838, 115.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe other half of the biological assembly is generated by: -X+1, 1/2-Y+1, Z.

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Components

#1: Protein transcription activator of multidrug-efflux transporter genes mta


Mass: 12861.807 Da / Num. of mol.: 1 / Fragment: N-terminus (Residues 1-109)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD-MYC-HIS / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P71039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: lithium chloride, magnesium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Godsey, M., (2000) Acta Crystallogr., D56, 1456.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 mg/mlprotein1drop
23.77 M1reservoirLiCl
350 mMHEPES1reservoirpH7.0
410 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1999
RadiationMonochromator: 58 cm long, Pt-coated, fused silica, vertical focus mirror; Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.75→23.3 Å / Num. all: 5246 / Num. obs: 5199 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 121.3 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.9
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.7 / Num. unique all: 377 / Rsym value: 0.271 / % possible all: 99
Reflection
*PLUS
% possible obs: 99.3 % / Num. measured all: 42297
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→23.33 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 157528.71 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC, RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 261 5.4 %RANDOM
Rwork0.2277 ---
all0.2311 4812 --
obs0.2311 4812 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.17 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 81.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å20 Å20 Å2
2--45.44 Å20 Å2
3----40.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.75→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 16 877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it3.121.5
X-RAY DIFFRACTIONc_mcangle_it4.72
X-RAY DIFFRACTIONc_scbond_it4.842
X-RAY DIFFRACTIONc_scangle_it6.822.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.088 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.527 36 5.2 %
Rwork0.4 654 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 81.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it3.121.5
X-RAY DIFFRACTIONc_scbond_it4.842
X-RAY DIFFRACTIONc_mcangle_it4.72
X-RAY DIFFRACTIONc_scangle_it6.822.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.527 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.4

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