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- PDB-1exi: CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTIL... -

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Basic information

Entry
Database: PDB / ID: 1exi
TitleCRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB
Components
  • DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')
  • MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
KeywordsTranscription/DNA / Protein-DNA complex / MerR-family transcription activator / multidrug-binding protein / Transcription-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 / MerR family regulatory protein / 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 / MerR family regulatory protein / 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
TETRAPHENYLANTIMONIUM ION / DNA / DNA (> 10) / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.12 Å
AuthorsZheleznova-Heldwein, E.E. / Brennan, R.G.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of the transcription activator BmrR bound to DNA and a drug.
Authors: Heldwein, E.E. / Brennan, R.G.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
M: DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')
A: MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9875
Polymers39,0612
Non-polymers9263
Water543
1
M: DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')
A: MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
hetero molecules

M: DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')
A: MULTIDRUG-EFFLUX TRANSPORTER REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,97410
Polymers78,1234
Non-polymers1,8526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_576x,-y+2,-z+3/21
Unit cell
Length a, b, c (Å)110.150, 110.150, 144.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

DetailsThe biological assembly is a dimer constructed from chain A by generating a two-fold symmetry partner. / The biological assembly is a DNA duplex constructed from chain B by generating a two-fold symmetry partner.

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3')


Mass: 6440.148 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein MULTIDRUG-EFFLUX TRANSPORTER REGULATOR / TRANSCRIPTION ACTIVATOR BMRR


Mass: 32621.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / References: UniProt: P39075
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-118 / TETRAPHENYLANTIMONIUM ION


Mass: 430.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20Sb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 5.61 Å3/Da / Density % sol: 78.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1imidazole11
2imidazole12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMprotein1drop
21 %DMSO1drop
31.0-1.2 Mimidazole1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.12→60.4 Å / Num. obs: 44719 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.7
Reflection shellResolution: 3.12→3.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.278 / % possible all: 78

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Processing

Software
NameClassification
TNTrefinement
bioteXdata reduction
bioteXdata scaling
TNTphasing
RefinementResolution: 3.12→16 Å / Cross valid method: throughtout / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.317 642 4.6 %RANDOM
Rwork0.268 ---
obs-14001 --
Refinement stepCycle: LAST / Resolution: 3.12→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 427 51 3 2593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg1.5
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 4.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.5

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