+Open data
-Basic information
Entry | Database: PDB / ID: 5ajs | ||||||
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Title | Crystal structure of a coiled-coil domain from human THAP11 | ||||||
Components | THAP DOMAIN-CONTAINING PROTEIN 11 | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR | ||||||
Function / homology | Function and homology information regulation of mitochondrial transcription / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin ...regulation of mitochondrial transcription / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cukier, C.D. / Maveyraud, L. / Milon, A. / Gervais, V. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: The C-Terminal Region of the Transcriptional Regulator Thap11 Forms a Parallel Coiled-Coil Domain Involved in Protein Dimerization. Authors: Cukier, C.D. / Maveyraud, L. / Saurel, O. / Guillet, V. / Milon, A. / Gervais, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ajs.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ajs.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ajs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajs_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 5ajs_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 5ajs_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 5ajs_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajs ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajs | HTTPS FTP |
-Related structure data
Related structure data | 1n6mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 8007.538 Da / Num. of mol.: 4 / Fragment: RESIDUES 247-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-20-THAP11 (201-314) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96EK4 #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: 2.53 Å3/Da / Density % sol: 51.4 % Description: THE COILED-COIL PART OF THE ENTRY 1N6M - AMINO- ACIDS 300-345 - WAS USED AS A SEARCH MODEL. |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M NA/K PHOSPHATE PH 6.2, 0.2 M NACL, 40% (V/V) MPD, HANGING DROP VAPOUR DIFFUSION, T = 285 K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014 / Details: TOROIDAL MIRROR | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→39.76 Å / Num. obs: 13992 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N6M Resolution: 2.3→39.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.336 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.591 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.76 Å
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Refine LS restraints |
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