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- PDB-4zs8: Crystal structure of ligand-free, full length DasR -

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Basic information

Entry
Database: PDB / ID: 4zs8
TitleCrystal structure of ligand-free, full length DasR
ComponentsHTH-type transcriptional repressor DasR
KeywordsTRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Winged helix-turn-helix motif / N-acetylglucosamine utilization / Ligand-free / Master regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional repressor DasR
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFillenberg, S.B. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Plos One / Year: 2016
Title: Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors.
Authors: Fillenberg, S.B. / Friess, M.D. / Korner, S. / Bockmann, R.A. / Muller, Y.A.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional repressor DasR
B: HTH-type transcriptional repressor DasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6447
Polymers57,3332
Non-polymers3105
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-1 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.033, 96.033, 118.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein HTH-type transcriptional repressor DasR


Mass: 28666.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: dasR, SCO5231, SC7E4.28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K492
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 26 % (w/v) PEG 400, 10 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17696 / % possible obs: 99.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA- and effector-binding domains of entry 2wv0

2wv0


Resolution: 2.6→44.522 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1060 5.99 %Random selection
Rwork0.201 ---
obs0.2055 17691 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 20 32 3697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083720
X-RAY DIFFRACTIONf_angle_d1.2175023
X-RAY DIFFRACTIONf_dihedral_angle_d15.4181439
X-RAY DIFFRACTIONf_chiral_restr0.042582
X-RAY DIFFRACTIONf_plane_restr0.006644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5994-2.71770.34762160.26831941X-RAY DIFFRACTION100
2.7177-2.86090.32291760.23971982X-RAY DIFFRACTION100
2.8609-3.04010.31281080.23382052X-RAY DIFFRACTION100
3.0401-3.27480.33511090.21892088X-RAY DIFFRACTION100
3.2748-3.60420.29881100.21252081X-RAY DIFFRACTION100
3.6042-4.12540.32431100.20422104X-RAY DIFFRACTION100
4.1254-5.19630.22281120.17122119X-RAY DIFFRACTION100
5.1963-44.52850.25491190.18932264X-RAY DIFFRACTION100

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