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- PDB-3eco: Crystal structure of MepR, a transcription regulator of the Staph... -

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Basic information

Entry
Database: PDB / ID: 3eco
TitleCrystal structure of MepR, a transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA
ComponentsMepR
KeywordsTRANSCRIPTION / mutlidrug efflux pump regulator winged helix-turn-helix motif / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
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
HTH marR-type domain-containing protein / HTH marR-type domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsBrennan, R.G. / Kumaraswami, M.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA.
Authors: Kumaraswami, M. / Schuman, J.T. / Seo, S.M. / Kaatz, G.W. / Brennan, R.G.
History
DepositionSep 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_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: MepR
B: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4813
Polymers32,3852
Non-polymers961
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-47 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.196, 96.574, 110.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MepR


Mass: 16192.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV0333 / Plasmid: pET101/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 star DE3 / References: UniProt: Q99WP3, UniProt: A0A0H3JPT9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 4000, 0.2 M Magnesium sulfate,10% glycerol, NDSB-256, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9797 0.9798 1.02
SYNCHROTRONALS 8.3.121.116
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97981
31.021
41.1161
ReflectionResolution: 2.4→500 Å / Num. all: 14202 / Num. obs: 14174 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.6

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Processing

Software
NameClassification
DENZOdata reduction
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→47.89 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1393 -Random
Rwork0.242 ---
all-14202 --
obs-14108 99.7 %-
Displacement parametersBiso mean: 1 Å2
Baniso -1Baniso -2Baniso -3
1-6.72 Å2-4.11 Å2-2.61 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 5 196 2327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1

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