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

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Basic information

Entry
Database: PDB / ID: 4wul
TitleCrystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 26bp DNA
Components
  • (DNA (26-MER)) x 2
  • 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: 2.4 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
DepositionNov 2, 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 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
H: DNA (26-MER)
C: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)31,3924
Polymers31,3924
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.585, 113.585, 48.225
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#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
Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R3G073, UniProt: D4EMQ0*PLUS
#2: DNA chain DNA (26-MER)


Mass: 8003.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)
#3: DNA chain DNA (26-MER)


Mass: 7967.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterococcus faecalis S613 (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.08 M KCl, 0.02 M BaCl2, 0.04 M Sodium cacodylate (pH 6.0), 43% MPD, 0.012 M Spermine tetrachloride, 0.01 M Proline, 0.01 M Strontium chloride

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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: 2.4→30 Å / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 22.5 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/av σ(I): 33.67 / Net I/σ(I): 33
Reflection shellResolution: 2.4→2.4 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 9.333 / Rsym value: 0.733 / % possible all: 100
Cell measurementReflection used: 280748

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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
Starting model: 4WTO

4wto
PDB Unreleased entry


Resolution: 2.4→29.445 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1334 9.98 %
Rwork0.2185 12030 -
obs0.224 13364 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.9 Å2 / Biso mean: 46.9647 Å2 / Biso min: 10.7 Å2
Refinement stepCycle: final / Resolution: 2.4→29.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 1066 0 98 2188
Biso mean---38.51 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042229
X-RAY DIFFRACTIONf_angle_d0.6863233
X-RAY DIFFRACTIONf_chiral_restr0.026378
X-RAY DIFFRACTIONf_plane_restr0.002231
X-RAY DIFFRACTIONf_dihedral_angle_d25.205890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4417-2.52890.3241350.261173130898
2.5289-2.63010.27891310.253511801311100
2.6301-2.74970.32561300.248111871317100
2.7497-2.89460.30451330.280912031336100
2.8946-3.07580.35311330.274212061339100
3.0758-3.3130.33231280.212111961324100
3.313-3.64580.26541340.203812061340100
3.6458-4.17210.29141310.18812051336100
4.1721-5.25150.21491340.195912221356100
5.2515-29.44680.22861450.208112521397100
Refinement TLS params.Method: refined / Origin x: 3.3254 Å / Origin y: 42.4077 Å / Origin z: -9.1498 Å
111213212223313233
T0.1416 Å20.0183 Å20.2302 Å2-0.219 Å20.0329 Å2--0.2422 Å2
L0.0366 °2-0.0069 °20.0216 °2-0.0445 °2-0.0204 °2--0.0717 °2
S0.1086 Å °0.0188 Å °-0.0214 Å °0.0013 Å °0.099 Å °-0.0034 Å °-0.0215 Å °0.0085 Å °0.1602 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA141 - 205
2X-RAY DIFFRACTION1allB142 - 205
3X-RAY DIFFRACTION1allH-124 - -99
4X-RAY DIFFRACTION1allC-99 - -124
5X-RAY DIFFRACTION1allS1 - 98

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