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- PDB-5d5z: Structure of Chaetomium thermophilum Skn7 coiled-coil domain, cry... -

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Basic information

Entry
Database: PDB / ID: 5d5z
TitleStructure of Chaetomium thermophilum Skn7 coiled-coil domain, crystal form II
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsNeudegger, T. / Verghese, J. / Hayer-Hartl, M. / Bracher, A. / Hartl, F.U.
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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcription factor
B: Putative transcription factor
C: Putative transcription factor
D: Putative transcription factor
E: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)28,5535
Polymers28,5535
Non-polymers00
Water2,180121
1
A: Putative transcription factor
B: Putative transcription factor
C: Putative transcription factor


Theoretical massNumber of molelcules
Total (without water)17,1323
Polymers17,1323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-52 kcal/mol
Surface area9040 Å2
MethodPISA
2
D: Putative transcription factor
E: Putative transcription factor

D: Putative transcription factor
E: 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 operation2_555-x,-y,z1
Buried area8680 Å2
ΔGint-85 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.004, 61.027, 75.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-319-

HOH

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Components

#1: Protein/peptide
Putative transcription factor / CtSkn7


Mass: 5710.513 Da / Num. of mol.: 5 / 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.: 121 / 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: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 21 % PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.7→47.53 Å / Num. obs: 24701 / % possible obs: 99.94 % / Redundancy: 8.8 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation47.53 Å2.8 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREP11.0.05phasing
REFMAC2.7.029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5Y

5d5y


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2988 / WRfactor Rwork: 0.2237 / FOM work R set: 0.7969 / SU B: 2.853 / SU ML: 0.096 / SU R Cruickshank DPI: 0.135 / SU Rfree: 0.1474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 1259 5.1 %RANDOM
Rwork0.2094 ---
obs0.2131 23400 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.01 Å2 / Biso mean: 34.714 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å2-0 Å2-0 Å2
2--0.19 Å20 Å2
3----2.65 Å2
Refinement stepCycle: final / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 121 2088
Biso mean---37.98 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021968
X-RAY DIFFRACTIONr_bond_other_d0.0030.021994
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9772644
X-RAY DIFFRACTIONr_angle_other_deg0.9873.0014567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9145244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.40428.46998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20315422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.732155
X-RAY DIFFRACTIONr_chiral_restr0.1340.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 96 -
Rwork0.308 1696 -
all-1792 -
obs--99.67 %

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