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- PDB-1r8e: Crystal Structure of BmrR Bound to DNA at 2.4A Resolution -

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Basic information

Entry
Database: PDB / ID: 1r8e
TitleCrystal Structure of BmrR Bound to DNA at 2.4A Resolution
Components
  • 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'
  • multidrug-efflux transporter regulator
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / MERR-FAMILY TRANSCRIPTION ACTIVATOR / MULTIDRUG-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Single helix bin / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. ...Single helix bin / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Regulatory factor, effector binding domain superfamily / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Barrel / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / TETRAPHENYLPHOSPHONIUM / DNA / DNA (> 10) / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNewberry, K.J. / Brennan, R.G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.
Authors: Newberry, K.J. / Brennan, R.G.
#1: Journal: Nature / Year: 2001
Title: Crystal structure of the transcription activator BmrR bound to DNA and a drug
Authors: Heldwein, E.E. / Brennan, R.G.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'
A: multidrug-efflux transporter regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,24019
Polymers39,6802
Non-polymers1,56017
Water2,360131
1
B: 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'
A: multidrug-efflux transporter regulator
hetero molecules

B: 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'
A: multidrug-efflux transporter regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,47938
Polymers79,3604
Non-polymers3,12034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)107.280, 107.280, 145.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

DetailsThe second part of the biological assembly is generate by the operations: x, -y, 1/2 - z

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Components

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DNA chain / Protein , 2 types, 2 molecules BA

#1: DNA chain 5'-D(*GP*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*TP*C)-3'


Mass: 7058.536 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein multidrug-efflux transporter regulator


Mass: 32621.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bmrr / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P39075

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Non-polymers , 4 types, 148 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P4P / TETRAPHENYLPHOSPHONIUM


Mass: 339.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20P
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 5.29 Å3/Da / Density % sol: 76.55 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1Imidazole11
2H2O11
3Imidazole12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 2002 / Details: single crystal monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→86.39 Å / Num. all: 33967 / Num. obs: 33613 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 50.9 Å2
Reflection shellResolution: 2.4→2.55 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXJ

1exj


Resolution: 2.4→86.39 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1694 5 %RANDOM
Rwork0.227 ---
obs0.227 33613 98.9 %-
all-33967 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.6217 Å2 / ksol: 0.349872 e/Å3
Displacement parametersBiso mean: 60.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.88 Å20 Å20 Å2
2--6.88 Å20 Å2
3----13.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 468 110 131 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it4.661.5
X-RAY DIFFRACTIONc_mcangle_it5.852
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it9.22.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 271 4.9 %
Rwork0.311 5289 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LIGANDS_PAR.TXTLIGANDS_TOP.TXT

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