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- PDB-3d70: Crystal structure of E253A mutant of BMRR bound to 22-bp oligonuc... -

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Basic information

Entry
Database: PDB / ID: 3d70
TitleCrystal structure of E253A mutant of BMRR bound to 22-bp oligonucleotide
Components
  • BMR promoter DNA
  • Multidrug-efflux transporter 1 regulator
KeywordsTRANSCRIPTION REGULATOR/DNA / MULTIDRUG RESISTANCE / TRANSCRIPTION REGULATION / PROTEIN-DNA COMPLEX / Activator / DNA-binding / TRANSCRIPTION REGULATOR-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Single helix bin / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : ...Single helix bin / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / 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 / 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 / DNA / DNA (> 10) / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNewberry, K.J. / Brennan, R.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion
Authors: Newberry, K.J. / Huffman, J.L. / Miller, M.C. / Vazquez-Laslop, N. / Neyfakh, A.A. / Brennan, R.G.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_entity_src_syn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BMR promoter DNA
B: Multidrug-efflux transporter 1 regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,47411
Polymers40,7832
Non-polymers6919
Water88349
1
A: BMR promoter DNA
B: Multidrug-efflux transporter 1 regulator
hetero molecules

A: BMR promoter DNA
B: Multidrug-efflux transporter 1 regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,94722
Polymers81,5664
Non-polymers1,38218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1,y,-z-11
Buried area15930 Å2
ΔGint-58.7 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.170, 106.170, 146.880
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-342-

HOH

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Components

#1: Protein BMR promoter DNA


Mass: 33420.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P39075
#2: DNA chain Multidrug-efflux transporter 1 regulator


Mass: 7362.729 Da / Num. of mol.: 1 / Fragment: residues 1-278 / Mutation: E253A, A277L, E278D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bmrR, bmr1R / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 5.3 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: SODIUM CITRATE, IMIDAZOLE, TRIFLUOROETHANOL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CITRATE11
2SODIUM CITRATE12
3IMIDAZOLE11
4IMIDAZOLE12
5TRIFLUOROETHANOL11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.8→52.5 Å / Num. obs: 20870 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 92.54 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.045 / Net I/σ(I): 12.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1531 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EXJ

1exj


Resolution: 2.8→52.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1318695.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1005 4.8 %RANDOM
Rwork0.234 ---
obs0.234 20807 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.31 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 70.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.2 Å20 Å20 Å2
2--8.2 Å20 Å2
3----16.41 Å2
Refinement stepCycle: LAST / Resolution: 2.8→52.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 468 48 49 2840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.2
X-RAY DIFFRACTIONc_mcangle_it7.18
X-RAY DIFFRACTIONc_scbond_it7.85
X-RAY DIFFRACTIONc_scangle_it10.3
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.576 152 4.4 %
Rwork0.445 3270 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.TOPPROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA.TOPDNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER.TOPWATER_REP.PARAM
X-RAY DIFFRACTION4LIGANDS_TOP.TXTLIGANDS_PAR.TXT
X-RAY DIFFRACTION5ION.TOPION.PARAM

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