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Yorodumi- PDB-6iir: Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iir | ||||||
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Title | Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA | ||||||
Components |
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Keywords | 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 | Function and homology information 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, Z. / Tian, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA Authors: Wang, Z. / Tian, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iir.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iir.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 6iir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iir_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 6iir_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 6iir_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6iir_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iir ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iir | HTTPS FTP |
-Related structure data
Related structure data | 6iipS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11578.261 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDGFL3, HDGF2, HDGFRP3, CGI-142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y3E1 #2: DNA chain | Mass: 3046.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 2.2 Å3/Da / Density % sol: 44.07 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 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: 2.2→50 Å / Num. obs: 12832 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 7 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 700 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IIP Resolution: 2.2→29.059 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 37.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.059 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: 56.163 Å / Origin y: -28.7894 Å / Origin z: -229.7076 Å
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Refinement TLS group | Selection details: all |