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- PDB-5d5w: Crystal structure of Chaetomium thermophilum Skn7 with HSE DNA -

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Basic information

Entry
Database: PDB / ID: 5d5w
TitleCrystal structure of Chaetomium thermophilum Skn7 with HSE DNA
Components
  • HSE DNA
  • Putative transcription factor
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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

Downloads & links

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Assembly

Deposited unit
A: HSE DNA
B: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)16,2802
Polymers16,2802
Non-polymers00
Water39622
1
A: HSE DNA
B: Putative transcription factor

A: HSE DNA
B: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)32,5614
Polymers32,5614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4840 Å2
ΔGint-25 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.771, 78.397, 90.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11B-207-

HOH

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Components

#1: DNA chain HSE DNA


Mass: 3662.404 Da / Num. of mol.: 1 / Fragment: DNA binding domain / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Putative transcription factor / CtSkn7


Mass: 12618.037 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 11 % PEG-3350, 0.18 M tri-Ammonium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97702 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 2.349→45.042 Å / Num. all: 6090 / Num. obs: 6090 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 61.1 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.051 / Rsym value: 0.045 / Net I/av σ(I): 9.6 / Net I/σ(I): 17.4 / Num. measured all: 28671
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.349-2.484.80.9580.842028700.4690.9581.899.2
2.48-2.634.60.561.438178280.2820.562.799.6
2.63-2.8150.3482.239537900.1680.3484.799.9
2.81-3.034.80.1744.535037280.0860.1748.399.8
3.03-3.324.60.0544.531356760.030.05415.498.3
3.32-3.714.90.0461329476070.0230.04625.298.5
3.71-4.294.50.03318.324135360.0170.03334.398.1
4.29-5.254.70.02622.322184680.0130.02644.698.5
5.25-7.434.30.02624.715983680.0130.02643.797
7.43-45.04240.01929.28852190.010.01952.396.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HTS

3hts


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2383 / WRfactor Rwork: 0.201 / FOM work R set: 0.6975 / SU B: 13.086 / SU ML: 0.277 / SU R Cruickshank DPI: 0.4434 / SU Rfree: 0.2592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 280 4.6 %RANDOM
Rwork0.2154 ---
obs0.2173 5791 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.63 Å2 / Biso mean: 72.272 Å2 / Biso min: 35.01 Å2
Baniso -1Baniso -2Baniso -3
1--6.22 Å20 Å20 Å2
2--4.6 Å2-0 Å2
3---1.62 Å2
Refinement stepCycle: final / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 243 0 22 1081
Biso mean---60.77 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0171112
X-RAY DIFFRACTIONr_bond_other_d0.0010.02915
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.7131544
X-RAY DIFFRACTIONr_angle_other_deg1.39732110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.563592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31722.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.215149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.042159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.712 23 -
Rwork0.455 411 -
all-434 -
obs--99.77 %

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