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- PDB-3q5r: Crystal structure of BmrR bound to Kanamycin -

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Basic information

Entry
Database: PDB / ID: 3q5r
TitleCrystal structure of BmrR bound to Kanamycin
Components
  • 23 bp promoter DNA
  • Multidrug-efflux transporter 1 regulator
KeywordsTRANSCRIPTION/RNA/ANTIBIOTIC / Multidrug binding / Multidrug resistance / Transcription regulator / TRANSCRIPTION-RNA-ANTIBIOTIC 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
KANAMYCIN A / DNA / DNA (> 10) / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBachas, S. / Eginton, C. / Gunio, G. / Wade, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR.
Authors: Bachas, S. / Eginton, C. / Gunio, D. / Wade, H.
History
DepositionDec 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug-efflux transporter 1 regulator
B: 23 bp promoter DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0213
Polymers40,5372
Non-polymers4841
Water0
1
A: Multidrug-efflux transporter 1 regulator
B: 23 bp promoter DNA
hetero molecules

A: Multidrug-efflux transporter 1 regulator
B: 23 bp promoter DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0426
Polymers81,0734
Non-polymers9692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area11380 Å2
ΔGint-99 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.891, 106.891, 145.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Details180 degree rotation on 2fold axis

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Components

#1: Protein Multidrug-efflux transporter 1 regulator


Mass: 33478.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bmrR, bmr1R, BSU24020 / Production host: Escherichia coli (E. coli) / References: UniProt: P39075
#2: DNA chain 23 bp promoter DNA


Mass: 7058.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 23 bp of the Bmr efflux gene synthesized by IDT
#3: Chemical ChemComp-KAN / KANAMYCIN A / Kanamycin A


Mass: 484.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM

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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: 5.13 Å3/Da / Density % sol: 76.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Sodium Malonate pH 7.0, 0.05% jeffamine M600, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.83→500 Å / Num. obs: 17370 / % possible obs: 83.4 %
Reflection shellResolution: 3.05→3.19 Å / % possible all: 69.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→44.24 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.12 / SU ML: 0.268 / SU R Cruickshank DPI: 0.6462 / Cross valid method: THROUGHOUT / ESU R: 0.639 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24672 711 4.8 %RANDOM
Rwork0.21083 ---
obs0.21259 13958 87.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.05→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 468 33 0 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7282.1993926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7745274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62924.095105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.251512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211949
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.51378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74222234
X-RAY DIFFRACTIONr_scbond_it2.11331443
X-RAY DIFFRACTIONr_scangle_it3.5294.51692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.051→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.56 29 -
Rwork0.434 538 -
obs--47.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3632-0.2611-1.4736.44922.01372.8723-0.25170.1592-0.33290.0629-0.01020.04990.1086-0.09010.2620.021-0.01830.02480.0325-0.01970.040445.501-21.20522.416
20.47760.13310.38230.3340.30310.75310.01250.04380.074-0.0373-0.0478-0.0123-0.0584-0.0180.03540.01150.01170.00580.02090.00710.025156.016-4.83227.688
30.82830.44360.18380.8289-0.1110.77770.0182-0.0502-0.06580.0163-0.05380.01030.07370.01460.03550.01290.00250.00890.00570.00480.016968.69923.16262.488
42.01330.631-0.13460.21480.03690.44270.0478-0.26190.09010.0271-0.13830.04710.0389-0.26850.09040.0415-0.03510.0010.2268-0.07930.032834.909-16.28533.115
53.2954-1.12430.06961.67351.0622.37660.18810.30960.2086-0.3724-0.2597-0.0156-0.1724-0.53880.07170.08930.0313-0.00060.16650.00650.016533.90318.50740.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 24
2X-RAY DIFFRACTION2A25 - 118
3X-RAY DIFFRACTION3A119 - 277
4X-RAY DIFFRACTION4B-12 - 1
5X-RAY DIFFRACTION5B2 - 12

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