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- PDB-1bl0: MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN (MARA)/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bl0
TitleMULTIPLE ANTIBIOTIC RESISTANCE PROTEIN (MARA)/DNA COMPLEX
Components
  • DNA (5'-D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP* CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP* TP*C)-3')
  • PROTEIN (MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTIONAL ACTIVATOR / A BIPARTITE HELIX-TURN-HELIX PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / sequence-specific DNA binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
: / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...: / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Multiple antibiotic resistance protein MarA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDavies, S. / Rhee, R.G. / Martin, J.L. / Rosner, D.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.
Authors: Rhee, S. / Martin, R.G. / Rosner, J.L. / Davies, D.R.
History
DepositionJul 22, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP* TP*C)-3')
C: DNA (5'-D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP* CP*C)-3')
A: PROTEIN (MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN)


Theoretical massNumber of molelcules
Total (without water)30,1813
Polymers30,1813
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 47.100, 298.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP* TP*C)-3')


Mass: 7458.828 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP* CP*C)-3') / MARA


Mass: 7280.704 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN)


Mass: 15441.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(LAMDADE3) / Gene: MARA / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): N8224 / References: UniProt: P0ACH5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG8000,100MM NA-CACODYLATE(PH8.0), 100MM CA-ACETATE, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium CACODYLATE11
2calcium ACETATE11
3PEG 800011
4PEG 800012
Crystal grow
*PLUS
Details: micro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG80001reservoir
2100 mMsodium cacodylate1reservoir
3100 mMcalcium acetate1reservoir
41

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16074 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.067
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5 % / Rsym value: 0.77 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 121112 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.77

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1241 10 %RANDOM
Rwork0.225 ---
obs0.225 12350 79.1 %-
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.2 Å20 Å20 Å2
2---10.2 Å20 Å2
3---21.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 978 0 144 2097
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.429 90 13.5 %
Rwork0.433 666 -
obs--39.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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