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- PDB-2bow: MULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 2bow
TitleMULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR IN COMPLEX WITH A LIGAND, TETRAPHENYLPHOSPHONIUM
ComponentsMULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
KeywordsTRANSCRIPTION ACTIVATOR / MULTIDRUG BINDING
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
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 / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...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 / Regulatory factor, effector binding domain superfamily / 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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / TETRAPHENYLPHOSPHONIUM / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZheleznova, E.E. / Markham, P.N. / Neyfakh, A.A. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter.
Authors: Zheleznova, E.E. / Markham, P.N. / Neyfakh, A.A. / Brennan, R.G.
History
DepositionAug 6, 1998Processing site: BNL
Revision 1.0Aug 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / software / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9824
Polymers18,4921
Non-polymers4903
Water19811
1
A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules

A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9658
Polymers36,9842
Non-polymers9816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area3510 Å2
ΔGint-22 kcal/mol
Surface area13930 Å2
MethodPISA, PQS
2
A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules

A: MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9658
Polymers36,9842
Non-polymers9816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area2420 Å2
ΔGint-43 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 82.600, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-160-

MN

21A-161-

SO4

31A-165-

HOH

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Components

#1: Protein MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR BMRR / BRC


Mass: 18492.049 Da / Num. of mol.: 1 / Fragment: MULTIDRUG-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P39075
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-P4P / TETRAPHENYLPHOSPHONIUM / Tetraphenylphosphonium chloride


Mass: 339.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTPP11
21.5 Mammonium sulfate11
30.1 Msodium cacodylate11pH6.5
45 %MPD11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→42.2 Å / Num. obs: 5322 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.083 / Net I/σ(I): 14.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.8 / % possible all: 90
Reflection
*PLUS
Num. measured all: 24335 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
EPMRphasing
TNT5Drefinement
bioteXdata reduction
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BOW

1bow


Resolution: 2.8→16 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO
RfactorNum. reflection% reflection
Rfree0.32 -10 %
all0.235 --
obs0.235 5285 95 %
Refinement stepCycle: LAST / Resolution: 2.8→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 31 11 1087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.72
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it4.03
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.326
Solvent computation
*PLUS
Displacement parameters
*PLUS

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