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- PDB-1jgs: Multiple Antibiotic Resistance Repressor, MarR -

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Basic information

Entry
Database: PDB / ID: 1jgs
TitleMultiple Antibiotic Resistance Repressor, MarR
ComponentsMULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARRMultiple drug resistance
KeywordsTRANSCRIPTION / Transcription regulation / DNA-binding / Repressor / Antibiotic resistance
Function / homology
Function and homology information


cellular response to antibiotic / response to heat / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Multiple antibiotic resistance protein MarR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsAlekshun, M.N. / Levy, S.B. / Mealy, T.R. / Seaton, B.A. / Head, J.F.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 A resolution.
Authors: Alekshun, M.N. / Levy, S.B. / Mealy, T.R. / Seaton, B.A. / Head, J.F.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7133
Polymers15,4361
Non-polymers2762
Water0
1
A: MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR
hetero molecules

A: MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4256
Polymers30,8732
Non-polymers5524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area5290 Å2
ΔGint-24 kcal/mol
Surface area15490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.000, 62.000, 132.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsDimer generated by crystallographic two fold rotation around an axis parallel to the x-axis.

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Components

#1: Protein MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARR / Multiple drug resistance


Mass: 15436.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27245
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG MME 5000, ammonium sulfate, sodium salicylate, heptanetriol, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: unknown / pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %(w/v)PEG5000 MME11
2200 mMammonium sulfate11
3100 mMcitrate11pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 6069 / % possible obs: 99.5 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 12 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 56495 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 12

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.287 506 random
Rwork0.247 --
all-6903 -
obs-5968 -
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 20 0 1098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.18
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3

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