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- PDB-6iiq: Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 6iiq | ||||||
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Title | Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3 / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() negative regulation of microtubule depolymerization / microtubule polymerization / tubulin binding / growth factor activity / neuron projection development / microtubule binding / chromatin remodeling / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Tian, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA Authors: Wang, Z. / Tian, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.6 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.1 KB | Display | ![]() |
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Full document | ![]() | 495 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iipS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11578.261 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 4894.239 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris, pH 8.0, 0.1 M sodium malonate, pH 8.0, and 26% polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 31501 / % possible obs: 94.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2 / Num. unique obs: 2046 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IIP Resolution: 1.85→28.972 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→28.972 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.2097 Å / Origin y: 7.9591 Å / Origin z: 50.1795 Å
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Refinement TLS group | Selection details: all |