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- PDB-3d71: Crystal structure of E253Q BMRR bound to 22 base pair promoter site -

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Basic information

Entry
Database: PDB / ID: 3d71
TitleCrystal structure of E253Q BMRR bound to 22 base pair promoter site
Components
  • BMR promoter DNA
  • Multidrug-efflux transporter 1 regulator
KeywordsTRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATOR / PROTEIN-DNA COMPLEX / MULTIDRUG BINDING PROTEIN / MERR FAMILY / WINGED-HELIX / Activator / DNA-binding / Transcription regulation / TRANSCRIPTION REGULATOR-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 / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / 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
TRIFLUOROETHANOL / CITRATE ANION / IMIDAZOLE / S-1,2-PROPANEDIOL / 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. / Huffman, J.L. / Brennan, R.G.
Citation
Journal: 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.
#1: 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.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,76813
Polymers40,8402
Non-polymers92811
Water99155
1
M: BMR promoter DNA
A: Multidrug-efflux transporter 1 regulator
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)83,53626
Polymers81,6804
Non-polymers1,85722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area16190 Å2
ΔGint-50.9 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.480, 105.480, 147.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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DNA chain / Protein , 2 types, 2 molecules MA

#1: DNA chain BMR promoter DNA


Mass: 7362.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Multidrug-efflux transporter 1 regulator


Mass: 33477.219 Da / Num. of mol.: 1 / Fragment: residues 1-278 / Mutation: E253Q, 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 / References: UniProt: P39075

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Non-polymers , 6 types, 66 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3F3O
#7: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 2001 / Details: MIRRORS
RadiationMonochromator: SILICON SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→47.2 Å / Num. obs: 20900 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.3 Å2 / Rsym value: 0.051 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.454 / % possible all: 99.9

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EXJ

1exj


Resolution: 2.8→47.17 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1072 5.1 %RANDOM
Rwork0.225 ---
obs0.225 20900 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.42 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 65.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.32 Å20 Å20 Å2
2--10.32 Å20 Å2
3----20.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 468 60 55 2868
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_deg1.3
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_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.85
X-RAY DIFFRACTIONc_mcangle_it3.15
X-RAY DIFFRACTIONc_scbond_it2.73
X-RAY DIFFRACTIONc_scangle_it4.26
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 184 5.4 %
Rwork0.329 3240 -
obs--99.5 %
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 DIFFRACTION4ION.TOPFLO_PAR.TXT
X-RAY DIFFRACTION5FLO_TOP.TXTION.PARAM

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