+Open data
-Basic information
Entry | Database: PDB / ID: 4pzn | ||||||
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Title | Crystal structure of PHC3 SAM L971E | ||||||
Components | Polyhomeotic-like protein 3 | ||||||
Keywords | DNA BINDING PROTEIN / SAM domain / Polycomb group / polymer / chromatin | ||||||
Function / homology | Function and homology information PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription ...PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / histone binding / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nanyes, D.R. / Junco, S.E. / Taylor, A.B. / Robinson, A.K. / Patterson, N.L. / Shivarajpur, A. / Halloran, J. / Hale, S.M. / Kaur, Y. / Hart, P.J. / Kim, C.A. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Multiple polymer architectures of human polyhomeotic homolog 3 sterile alpha motif. Authors: Nanyes, D.R. / Junco, S.E. / Taylor, A.B. / Robinson, A.K. / Patterson, N.L. / Shivarajpur, A. / Halloran, J. / Hale, S.M. / Kaur, Y. / Hart, P.J. / Kim, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pzn.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pzn.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 4pzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzn ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzn | HTTPS FTP |
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-Related structure data
Related structure data | 4pzoC 1kw4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9465.790 Da / Num. of mol.: 5 / Fragment: sterile alpha motif / Mutation: L971E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EDR3, PH3, PHC3 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q8NDX5 #2: Chemical | ChemComp-EDO / #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: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 55% ethylene glycol, 100 mM tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Oct 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.68 Å / Num. obs: 19834 / % possible obs: 97.8 % / Redundancy: 2 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.029 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2873 / Rsym value: 0.253 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KW4 Resolution: 2.3→19.683 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.52 / Stereochemistry target values: ML
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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: 57.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.683 Å
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Refine LS restraints |
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LS refinement shell |
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