+Open data
-Basic information
Entry | Database: PDB / ID: 6iip | ||||||
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Title | Apo-form structure of the HRP3 PWWP domain | ||||||
Components | Hepatoma-derived growth factor-related protein 3 | ||||||
Keywords | DNA BINDING PROTEIN / growth factor / PWWP domain / Hepatoma-derived growth factor-related protein 3 | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.951 Å | ||||||
Authors | Wang, Z. / Tian, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Apo-form structure of the HRP3 PWWP domain 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 | 6iip.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iip.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 6iip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iip_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 6iip_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 6iip_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 6iip_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iip ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iip | HTTPS FTP |
-Related structure data
Related structure data | 3eaeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10112.490 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: Chemical | #3: Chemical | ChemComp-SO4 / #4: 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: 1.85 Å3/Da / Density % sol: 33.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulphate, 0.1 M MES monohydrate, pH 6.5, and 30% w/v polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91531 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91531 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 93005 / % possible obs: 97.4 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 52.6 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4036 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EAE Resolution: 0.951→30.876 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.951→30.876 Å
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Refine LS restraints |
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LS refinement shell |
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