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- PDB-5d5y: Structure of Chaetomium thermophilum Skn7 coiled-coil domain, cry... -

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Basic information

Entry
Database: PDB / ID: 5d5y
TitleStructure of Chaetomium thermophilum Skn7 coiled-coil domain, crystal form I
ComponentsPutative transcription factor
KeywordsTRANSCRIPTION / coiled-coil
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor SKN7
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.03 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 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
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
B: Putative transcription factor
A: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)11,4212
Polymers11,4212
Non-polymers00
Water2,252125
1
B: Putative transcription factor
A: Putative transcription factor

B: Putative transcription factor
A: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)22,8424
Polymers22,8424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9250 Å2
ΔGint-92 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.823, 151.535, 47.745
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-193-

ARG

21A-335-

HOH

31A-360-

HOH

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Components

#1: Protein/peptide Putative transcription factor / CtSkn7


Mass: 5710.513 Da / Num. of mol.: 2 / Fragment: UNP residues 160-209
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 % PEG-6000, 0.1 M HEPES-NaOH pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 44.8 % / Number: 311621 / Rmerge(I) obs: 0.079 / D res high: 1.95 Å / D res low: 47.74 Å / Num. obs: 6952 / % possible obs: 99.4 / Rejects: 9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.95210.76922.7
8.9347.7410.04739.8
ReflectionResolution: 1.03→40.39 Å / Num. obs: 45013 / % possible obs: 98.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.02 / Net I/σ(I): 17.1 / Num. measured all: 514459
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
1.03-1.055.41.1031.5964217710.680.49580.8
5.63-40.3910.10.06640.134913460.9960.02399.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
SHELXphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.03→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.1629 / FOM work R set: 0.8776 / SU B: 0.815 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0294 / SU Rfree: 0.0316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2257 5 %RANDOM
Rwork0.1648 ---
obs0.1664 42643 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.27 Å2 / Biso mean: 21.26 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20 Å2
2--0.23 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 127 913
Biso mean---32.74 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019858
X-RAY DIFFRACTIONr_bond_other_d0.0030.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9831165
X-RAY DIFFRACTIONr_angle_other_deg0.9853.0021988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5225114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.562840
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47115184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.264153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021029
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02186
X-RAY DIFFRACTIONr_rigid_bond_restr6.91231721
X-RAY DIFFRACTIONr_sphericity_free33.47528
X-RAY DIFFRACTIONr_sphericity_bonded15.21951812
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 149 -
Rwork0.355 2820 -
all-2969 -
obs--90.99 %

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