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- PDB-4zsi: Crystal structure of the effector-binding domain of DasR (DasR-EB... -

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Basic information

Entry
Database: PDB / ID: 4zsi
TitleCrystal structure of the effector-binding domain of DasR (DasR-EBD) in complex with glucosamine-6-phosphate
ComponentsHTH-type transcriptional repressor DasR
KeywordsTRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Effector-binding domain / N-acetylglucosamine utilization / Master regulator / Glucosamine-6-phosphate
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
Chem-4R1 / Chem-GLP / HTH-type transcriptional repressor DasR
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsFillenberg, S.B. / Koerner, S. / 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 1.2Jul 29, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: HTH-type transcriptional repressor DasR
B: HTH-type transcriptional repressor DasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9586
Polymers38,3162
Non-polymers6424
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-5 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.267, 54.267, 220.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

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Components

#1: Protein HTH-type transcriptional repressor DasR


Mass: 19157.867 Da / Num. of mol.: 2 / Fragment: UNP residues 88-254
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: Sugar ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-4R1 / 2-amino-2-deoxy-6-O-phosphono-beta-D-glucopyranose / beta-glucosamine-6-phosphate / 6-O-phosphono-beta-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-beta-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 259.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO8P
IdentifierTypeProgram
b-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M potassium thiocyanate and 30 % (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: 1.65→35 Å / Num. obs: 46439 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 21
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.1 / % 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: Effector-binding domain of entry 2wv0

2wv0


Resolution: 1.652→27.133 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 2310 4.97 %Random selection
Rwork0.1896 ---
obs0.1917 46436 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.652→27.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 40 279 2911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072691
X-RAY DIFFRACTIONf_angle_d1.0963645
X-RAY DIFFRACTIONf_dihedral_angle_d13.7931033
X-RAY DIFFRACTIONf_chiral_restr0.04428
X-RAY DIFFRACTIONf_plane_restr0.004462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6524-1.68610.31571350.28372549X-RAY DIFFRACTION100
1.6861-1.72270.30061320.25552509X-RAY DIFFRACTION100
1.7227-1.76280.27531350.24742564X-RAY DIFFRACTION100
1.7628-1.80690.29051360.23122590X-RAY DIFFRACTION100
1.8069-1.85570.27491320.21862520X-RAY DIFFRACTION100
1.8557-1.91030.2411350.20122568X-RAY DIFFRACTION100
1.9103-1.9720.2411310.1982545X-RAY DIFFRACTION100
1.972-2.04240.21491360.19442580X-RAY DIFFRACTION100
2.0424-2.12420.24411330.19362571X-RAY DIFFRACTION100
2.1242-2.22080.20041350.19332569X-RAY DIFFRACTION100
2.2208-2.33780.2481370.1882614X-RAY DIFFRACTION100
2.3378-2.48420.24781370.19132603X-RAY DIFFRACTION100
2.4842-2.67580.25771360.2072596X-RAY DIFFRACTION100
2.6758-2.94480.21531370.20882609X-RAY DIFFRACTION100
2.9448-3.37030.25731390.1872657X-RAY DIFFRACTION100
3.3703-4.24360.20441380.16762649X-RAY DIFFRACTION99
4.2436-27.13710.20871460.16652833X-RAY DIFFRACTION99

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