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Yorodumi- PDB-7m5w: Crystal structure of the HMG-C1 domain of human capicua bound to DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m5w | ||||||
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Title | Crystal structure of the HMG-C1 domain of human capicua bound to DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / helix-turn-helix / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II ...social behavior / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Model details | HMG box, HTH, DNA complex | ||||||
Authors | Webb, J.P. / Liew, J.J.M. / Gnann, A.D. / Dowling, D.P. | ||||||
Citation | Journal: Biorxiv / Year: 2022 Title: Molecular basis of DNA recognition by the HMG-box-C1 module of Capicua Authors: Webb, J. / Gnann, A.D. / Liew, J.J. / Patterson, M. / Paul, S. / Fores, M. / Jimenez, G. / Veraksa, A. / Dowling, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m5w.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m5w.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 7m5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/7m5w ftp://data.pdbj.org/pub/pdb/validation_reports/m5/7m5w | HTTPS FTP |
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-Related structure data
Related structure data | 2jrpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21962.199 Da / Num. of mol.: 1 Fragment: HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CIC, KIAA0306 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q96RK0 |
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#2: DNA chain | Mass: 5612.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ThermoFisher Custom DNA Oligo Synthesis / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5416.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ThermoFisher Custom DNA Oligo Synthesis / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527. Residue F95 was ...HMG box domain UNP residues 188-280 fused with C1 domain UNP residues 1457-1527. Residue F95 was inserted within the flexible linker region to increase UV absorption properties for purification. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.7 % / Description: orthorhombic |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES, 100 mM CaCl2, 100 mM NaCl, and 16% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 31, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→23.844 Å / Num. obs: 8838 / % possible obs: 98.8 % / Redundancy: 8.943 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.088 / Χ2: 0.864 / Net I/σ(I): 22.47 / Num. measured all: 79037 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2JRP Resolution: 2.95→23.84 Å / SU ML: 0.2704 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.0489 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→23.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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