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- PDB-3d6z: Crystal structure of R275E mutant of BMRR bound to DNA and rhodamine -

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Basic information

Entry
Database: PDB / ID: 3d6z
TitleCrystal structure of R275E mutant of BMRR bound to DNA and rhodamine
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
RHODAMINE 6G / 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: 2.6 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 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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)41,6257
Polymers40,8132
Non-polymers8125
Water1,54986
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)83,25014
Polymers81,6264
Non-polymers1,62410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area15970 Å2
ΔGint-100.5 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.500, 106.500, 146.140
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 (E. coli) / Strain (production host): TOP10 / References: UniProt: P39075
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-RHQ / RHODAMINE 6G / Rhodamine 6G


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 7
Details: SODIUM MALONATE, JEFFAMINE-M600, pH 7.00, 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 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2004
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→52.4 Å / Num. obs: 26429 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 69.57 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.046 / Net I/σ(I): 18.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3783 / Rsym value: 0.436 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNSrefinement
ADSCQuantumdata collection
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R8E

1r8e


Resolution: 2.6→52.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1924845.75 / 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
Rfree0.263 1275 4.8 %RANDOM
Rwork0.226 ---
obs0.226 26413 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.66 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 61 Å2
Baniso -1Baniso -2Baniso -3
1-7.06 Å20 Å20 Å2
2--7.06 Å20 Å2
3----14.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 488 57 86 2919
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_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.72
X-RAY DIFFRACTIONc_mcangle_it6.59
X-RAY DIFFRACTIONc_scbond_it7.31
X-RAY DIFFRACTIONc_scangle_it9.37
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 215 5 %
Rwork0.352 4077 -
obs--99.3 %
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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