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- PDB-4zsb: Crystal structure of the ligand-free effector-binding domain of D... -

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Basic information

Entry
Database: PDB / ID: 4zsb
TitleCrystal structure of the ligand-free effector-binding domain of DasR (DasR-EBD)
ComponentsHTH-type transcriptional repressor DasR
KeywordsTRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Effector-binding domain / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional repressor DasR
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsFillenberg, S.B. / Grau, F.C. / 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


Theoretical massNumber of molelcules
Total (without water)19,0291
Polymers19,0291
Non-polymers00
Water1,35175
1
A: HTH-type transcriptional repressor DasR

A: HTH-type transcriptional repressor DasR


Theoretical massNumber of molelcules
Total (without water)38,0572
Polymers38,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.634, 56.634, 108.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

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Components

#1: Protein HTH-type transcriptional repressor DasR


Mass: 19028.689 Da / Num. of mol.: 1 / Fragment: UNP residues 89-254
Source method: isolated from a genetically manipulated source
Details: DasR-EBD comprises residues 88-254 of full-length DasR
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: dasR, SCO5231, SC7E4.28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K492
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bis-Tris propane pH 9.0, 4.0 M potassium formate, 20 % (w/v) PEG monomethyl ether 2,000

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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: Feb 2, 2011
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→50 Å / Num. obs: 14018 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.4 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Effector-binding domain of entry 2wv0

2wv0


Resolution: 2.004→44.727 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1288 5.05 %Random selection
Rwork0.2122 ---
obs0.2145 14016 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.004→44.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 0 75 1350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091308
X-RAY DIFFRACTIONf_angle_d1.1011773
X-RAY DIFFRACTIONf_dihedral_angle_d15.017505
X-RAY DIFFRACTIONf_chiral_restr0.043205
X-RAY DIFFRACTIONf_plane_restr0.005229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.004-2.08420.34031330.33812410X-RAY DIFFRACTION86
2.0842-2.17910.30181430.28722713X-RAY DIFFRACTION97
2.1791-2.2940.3591370.26162705X-RAY DIFFRACTION99
2.294-2.43770.30271440.25122781X-RAY DIFFRACTION100
2.4377-2.62590.34461450.24852748X-RAY DIFFRACTION99
2.6259-2.89010.27161480.232745X-RAY DIFFRACTION99
2.8901-3.30820.26571470.21242772X-RAY DIFFRACTION99
3.3082-4.16750.22051500.19742674X-RAY DIFFRACTION98
4.1675-44.73790.21441410.16952669X-RAY DIFFRACTION96

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