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- PDB-9i7a: Crystal structure of HRP-2 PWWP domain with C64S mutation - Cryst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9i7a | ||||||||||||
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Title | Crystal structure of HRP-2 PWWP domain with C64S mutation - Crystal form P1 type 1 | ||||||||||||
![]() | Hepatoma-derived growth factor-related protein 2 | ||||||||||||
![]() | GENE REGULATION / Epigenetics | ||||||||||||
Function / homology | ![]() histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination ...histone H3K27me3 reader activity / skeletal muscle tissue regeneration / muscle cell differentiation / histone H3K9me2/3 reader activity / muscle organ development / DNA repair-dependent chromatin remodeling / histone reader activity / positive regulation of double-strand break repair via homologous recombination / positive regulation of cell growth / DNA recombination / chromatin remodeling / DNA repair / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Vantieghem, T. / Osipov, E.M. / Strelkov, S.V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal engineering of the hepatoma-derived growth factor-related protein 2 PWWP domain towards crystallographic fragment screening. Authors: Vantieghem, T. / Osipov, E.M. / Beelen, S. / Strelkov, S.V. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167 KB | Display | ![]() |
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PDB format | ![]() | 132.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9i7bC ![]() 9i7cC ![]() 9i7dC ![]() 9i7eC ![]() 9i7fC ![]() 9i7gC ![]() 9i7hC ![]() 9i7iC ![]() 9i7jC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 10698.171 Da / Num. of mol.: 2 / Mutation: C64S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.4 M ammonium acetate pH 5.0 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→36.66 Å / Num. obs: 85077 / % possible obs: 88.6 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Χ2: 0.93 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.05→1.11 Å / % possible obs: 66.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 1.257 / Num. measured all: 49819 / Num. unique obs: 9337 / CC1/2: 0.672 / Rpim(I) all: 0.573 / Rrim(I) all: 1.388 / Χ2: 0.66 / Net I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.452 Å2
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Refinement step | Cycle: 1 / Resolution: 1.05→36.65 Å
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Refine LS restraints |
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