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Yorodumi- PDB-5d60: Structure of Chaetomium thermophilum Skn7 coiled-coil domain, cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d60 | ||||||
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Title | Structure of Chaetomium thermophilum Skn7 coiled-coil domain, crystal form III | ||||||
Components | Putative transcription factor | ||||||
Keywords | TRANSCRIPTION / 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 | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d60.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d60.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 5d60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d60_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 5d60_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 5d60_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 5d60_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d60 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d60 | HTTPS FTP |
-Related structure data
Related structure data | 5d5uC 5d5vC 5d5wC 5d5xC 5d5ySC 5d5zC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 6945.839 Da / Num. of mol.: 4 / Fragment: UNP residues 160-220 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25 % PEG-3350, 0.2 M MgCl2 and 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.9→44.55 Å / Num. obs: 14684 / % possible obs: 97.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.048 / Net I/σ(I): 7.2 / Num. measured all: 41428 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D5Y Resolution: 1.9→44.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2975 / WRfactor Rwork: 0.2387 / FOM work R set: 0.7883 / SU B: 3.939 / SU ML: 0.12 / SU R Cruickshank DPI: 0.0556 / SU Rfree: 0.0454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.6 Å2 / Biso mean: 45.994 Å2 / Biso min: 17.98 Å2
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Refinement step | Cycle: final / Resolution: 1.9→44.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.896→1.945 Å / Total num. of bins used: 20
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