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- PDB-5ae4: Structures of inactive and activated DntR provide conclusive evid... -

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Basic information

Entry
Database: PDB / ID: 5ae4
TitleStructures of inactive and activated DntR provide conclusive evidence for the mechanism of action of LysR transcription factors
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION / LYSR-TYPE TRANSCRIPTION REGULATORS / LTTR / TRANSCRIPTION FACTOR / HELIX-TURN-HELIX / DNA BINDING PROTEIN / ROSSMANN-LIKE FOLD / AUTOINDUCING MUTANT / H169T-DNTR
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA CEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLerche, M. / Dian, C. / Round, A. / Lonneborg, R. / Brzezinski, P. / Leonard, G.A.
CitationJournal: Sci.Rep. / Year: 2016
Title: The Solution Configurations of Inactive and Activated Dntr Have Implications for the Sliding Dimer Mechanism of Lysr Transcription Factors.
Authors: Lerche, M. / Dian, C. / Round, A. / Lonneborg, R. / Brzezinski, P. / Leonard, G.A.
History
DepositionAug 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSR-TYPE REGULATORY PROTEIN
B: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7874
Polymers69,6702
Non-polymers1162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-30.8 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.472, 107.472, 297.771
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein LYSR-TYPE REGULATORY PROTEIN / DNTR


Mass: 34835.242 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: Q7WT50
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS

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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: 3.57 Å3/Da / Density % sol: 65.57 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M SODIUM TARTRATE, 0.2 M POTASSIUM THIOCYANATE 0.1 M TRIS-HCL PH 8.5, 20 % (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→43.57 Å / Num. obs: 16127 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 79.03 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.9
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTB

1utb


Resolution: 3.3→43.57 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 812 5.1 %
Rwork0.1882 --
obs0.1908 16041 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.2 Å2
Refinement stepCycle: LAST / Resolution: 3.3→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 6 0 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043436
X-RAY DIFFRACTIONf_angle_d0.8634668
X-RAY DIFFRACTIONf_dihedral_angle_d14.4391249
X-RAY DIFFRACTIONf_chiral_restr0.058517
X-RAY DIFFRACTIONf_plane_restr0.004611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.50670.31441410.25992458X-RAY DIFFRACTION100
3.5067-3.77730.25181390.20392481X-RAY DIFFRACTION100
3.7773-4.15720.22131310.16922496X-RAY DIFFRACTION100
4.1572-4.75810.17351350.14012512X-RAY DIFFRACTION100
4.7581-5.99230.23581170.1732583X-RAY DIFFRACTION99
5.9923-43.57430.27481490.21442699X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7865-0.56890.20180.2665-0.29860.56140.0661-0.0563-0.02250.0159-0.0536-0.0179-0.2990.0833-0.04930.43220.02160.01390.1579-0.06930.3458-6.574223.6669-13.4037
20.519-0.42110.16690.56360.17850.69460.08040.06640.0647-0.0524-0.0403-0.0769-0.4353-0.08660.00640.42720.11850.04510.22790.0120.3717-22.128729.554-29.3949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 89 THROUGH 303 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 88 THROUGH 300 )

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