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- PDB-3d6y: Crystal structure of R275E mutant of BMRR bound to DNA and berberine -

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Basic information

Entry
Database: PDB / ID: 3d6y
TitleCrystal structure of R275E mutant of BMRR bound to DNA and berberine
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 / 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
BERBERINE / DNA / DNA (> 10) / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 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 / _entity_src_gen.pdbx_host_org_scientific_name / _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
B: BMR promoter DNA
A: Multidrug-efflux transporter 1 regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3335
Polymers40,8132
Non-polymers5213
Water61334
1
B: BMR promoter DNA
A: Multidrug-efflux transporter 1 regulator
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)82,66710
Polymers81,6264
Non-polymers1,0416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area14530 Å2
ΔGint-92.3 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.330, 106.330, 146.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#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: 33450.121 Da / Num. of mol.: 1 / Fragment: residues 1-278 / Mutation: R275E, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39075
#3: Chemical ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 5.081581 Å3/Da / Density % sol: 75.794937 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Sodium Malonate, 0.05% Jeffamine-M600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Malonate11
2Sodium Malonate12
3Jeffamine-M60011
4Jeffamine-M60012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→86.1 Å / Num. obs: 23429 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 78.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.057 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3331 / Rsym value: 0.544 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MIR
Starting model: PDB entry 1R8D

1r8d


Resolution: 2.7→86.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1684928.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1132 4.8 %RANDOM
Rwork0.227 ---
obs0.227 23429 98.3 %-
all-23804 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.1095 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 82.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.73 Å20 Å20 Å2
2--10.73 Å20 Å2
3----21.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→86.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 488 37 34 2847
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.571.5
X-RAY DIFFRACTIONc_mcangle_it5.52
X-RAY DIFFRACTIONc_scbond_it5.422
X-RAY DIFFRACTIONc_scangle_it7.432.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 190 5 %
Rwork0.375 3637 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.param
X-RAY DIFFRACTION5ligands_par.txtligands_top.txt
X-RAY DIFFRACTION4dna-rna.top

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