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- PDB-5d5x: Crystal structure of Chaetomium thermophilum Skn7 with SSRE DNA -

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Basic information

Entry
Database: PDB / ID: 5d5x
TitleCrystal structure of Chaetomium thermophilum Skn7 with SSRE DNA
Components
  • Putative transcription factor
  • SSRE DNA strand 1
  • SSRE DNA strand 2
KeywordsTRANSCRIPTION / protein-DNA complex / double helix / helix-turn-helix
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity / identical protein binding / nucleus
Similarity search - Function
HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 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 / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor SKN7
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNeudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of human heat-shock transcription factor 1 in complex with DNA.
Authors: Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Structure summary
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: SSRE DNA strand 1
D: SSRE DNA strand 2
B: Putative transcription factor
E: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)33,1804
Polymers33,1804
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-24 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.733, 43.328, 88.780
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-206-

HOH

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Components

#1: DNA chain SSRE DNA strand 1


Mass: 3945.589 Da / Num. of mol.: 1 / Fragment: DNA binding domain / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: DNA chain SSRE DNA strand 2


Mass: 3998.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Protein Putative transcription factor / CtSkn7


Mass: 12618.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0048700 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SB31
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25 % PEG-2000 MME, 0.1 M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.39→44.34 Å / Num. obs: 11227 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.045 / Net I/σ(I): 10.5 / Num. measured all: 56918
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.39-2.484.50.7931.7490610950.6430.41194
8.94-44.344.40.05126.510462370.9960.02699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5W

5d5w


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2814 / WRfactor Rwork: 0.2249 / FOM work R set: 0.7616 / SU B: 11.464 / SU ML: 0.269 / SU R Cruickshank DPI: 0.6397 / SU Rfree: 0.3232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.64 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 532 4.8 %RANDOM
Rwork0.2279 ---
obs0.2311 10639 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.52 Å2 / Biso mean: 50.29 Å2 / Biso min: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å21.03 Å2
2---1.08 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 527 0 39 2237
Biso mean---41.22 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0172311
X-RAY DIFFRACTIONr_bond_other_d0.0020.021860
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.7033222
X-RAY DIFFRACTIONr_angle_other_deg1.24134287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37622.92999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65415292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.791514
X-RAY DIFFRACTIONr_chiral_restr0.080.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.529 42 -
Rwork0.379 750 -
all-792 -
obs--99.75 %

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