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- PDB-4wu4: Crystal structure of E. faecalis DNA binding domain LiaRD191N com... -

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Basic information

Entry
Database: PDB / ID: 4wu4
TitleCrystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 22bp DNA
Components
  • DNA (5'-D(P*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-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: 2.3 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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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*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0186
Polymers25,8344
Non-polymers1842
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-43 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.336, 77.248, 104.987
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 Response regulator receiver domain protein / Response regulator


Mass: 7710.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R3G073, UniProt: D4EMQ0*PLUS
#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*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3')


Mass: 5161.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.03 M Bis-Tris propane /3.4, 0.07 M Citric acid, 18% PEG 3,350, 0.05% LDAO, 0.1 M Sodium malonate.
PH range: 8.4-8.6

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 26
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 2.667 / Rsym value: 0.904 / % possible all: 99.2
Cell measurementReflection used: 197972

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.74 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 1316 10.03 %
Rwork0.208 --
obs0.214 13117 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 697 12 102 1891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031881
X-RAY DIFFRACTIONf_angle_d0.6022677
X-RAY DIFFRACTIONf_dihedral_angle_d22.668739
X-RAY DIFFRACTIONf_chiral_restr0.026316
X-RAY DIFFRACTIONf_plane_restr0.002220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3041-2.39630.3711920.2681858X-RAY DIFFRACTION59
2.3963-2.50530.30041160.2561028X-RAY DIFFRACTION75
2.5053-2.63730.33051390.2331266X-RAY DIFFRACTION89
2.6373-2.80240.28211560.24351376X-RAY DIFFRACTION97
2.8024-3.01860.29781570.24711403X-RAY DIFFRACTION98
3.0186-3.3220.30291590.21841418X-RAY DIFFRACTION100
3.322-3.80170.2311600.1851440X-RAY DIFFRACTION100
3.8017-4.78620.21011650.16691478X-RAY DIFFRACTION100
4.7862-28.73930.25151720.20581534X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.4251 Å / Origin y: -2.1861 Å / Origin z: 5.0884 Å
111213212223313233
T0.0952 Å20.0095 Å2-0.0341 Å2-0.0739 Å20.0145 Å2--0.0941 Å2
L0.7717 °20.4794 °2-0.8635 °2-0.4875 °21.245 °2--1.3579 °2
S-0.0631 Å °-0.0221 Å °0.1273 Å °0.037 Å °0.0323 Å °0.125 Å °-0.0416 Å °0.1463 Å °-0.0149 Å °
Refinement TLS groupSelection details: ALL

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