+Open data
-Basic information
Entry | Database: PDB / ID: 4pzo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PHC3 SAM L967R | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pzo.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pzo.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzo ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzo | HTTPS FTP |
---|
-Related structure data
Related structure data | 4pznSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9569.988 Da / Num. of mol.: 6 / Fragment: sterile alpha motif / Mutation: L967R 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.11 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.64 Å / Num. obs: 32712 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4722 / Rsym value: 0.476 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PZN Resolution: 2.25→40.557 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 47.64 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→40.557 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|