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- PDB-4wuh: Crystal structure of E. faecalis DNA binding domain LiaR wild typ... -

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Basic information

Entry
Database: PDB / ID: 4wuh
TitleCrystal structure of E. faecalis DNA binding domain LiaR wild type complexed with 22bp DNA
Components
  • DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3')
  • DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')
  • Response regulator receiver domain proteinResponse regulator
KeywordsDNA BINDING PROTEIN/DNA / helix-turn-helix / response regulator / enterococci / DNA binding domain / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Response regulator receiver domain protein
Similarity search - Component
Biological speciesEnterococcus faecalis S613 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.294 Å
AuthorsDavlieva, M. / Shamoo, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI080714 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin.
Authors: Davlieva, M. / Shi, Y. / Leonard, P.G. / Johnson, T.A. / Zianni, M.R. / Arias, C.A. / Ladbury, J.E. / Shamoo, Y.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Experimental preparation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.5Dec 27, 2023Group: 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
A: Response regulator receiver domain protein
B: Response regulator receiver domain protein
G: DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3')
H: DNA (5'-D(P*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')
C: DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9737
Polymers25,7895
Non-polymers1842
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-45 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.332, 77.932, 104.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Response regulator receiver domain protein / Response regulator


Mass: 7710.860 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis S613 (bacteria) / Strain: S613 / Gene: HMPREF9376_01931 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D4EMQ0

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DNA chain , 3 types, 3 molecules GHC

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


Mass: 5250.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)
#3: DNA chain DNA (5'-D(P*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')


Mass: 3299.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)
#4: DNA chain DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3')


Mass: 1817.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)

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Non-polymers , 2 types, 123 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.2 M Magnesium formate dihydrate, 20%w/v PEG 3,350, 0.012 M Spermine tetrachloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2013 / Details: Bimorph K-B pair
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/av σ(I): 25.258 / Net I/σ(I): 25
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 7.176 / Rsym value: 0.431 / % possible all: 100
Cell measurementReflection used: 206189

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.294→28.746 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 2662 10.03 %
Rwork0.2146 23874 -
obs0.219 26536 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.76 Å2 / Biso mean: 35.1498 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 2.294→28.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 697 12 121 1910
Biso mean--51.16 35.55 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041881
X-RAY DIFFRACTIONf_angle_d0.6382677
X-RAY DIFFRACTIONf_chiral_restr0.025316
X-RAY DIFFRACTIONf_plane_restr0.002220
X-RAY DIFFRACTIONf_dihedral_angle_d21.737739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2941-2.33580.29291230.25141072119585
2.3358-2.38080.30391330.24661173130690
2.3808-2.42930.27091310.24041216134793
2.4293-2.48210.28021350.24511228136396
2.4821-2.53980.29311440.23621254139898
2.5398-2.60330.24911440.22311257140199
2.6033-2.67360.27791470.235612771424100
2.6736-2.75230.22261460.234712891435100
2.7523-2.8410.31881420.241612581400100
2.841-2.94250.28851480.228713141462100
2.9425-3.06010.26441320.236412491381100
3.0601-3.19920.27951500.22313231473100
3.1992-3.36770.24331400.22641261140199
3.3677-3.57830.24441380.202312741412100
3.5783-3.8540.27431460.20051294144099
3.854-4.24070.21781440.174912811425100
4.2407-4.85180.21141380.176712961434100
4.8518-6.10320.30271400.216312701410100
6.1032-28.74840.24991410.216212881429100

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