+Open data
-Basic information
Entry | Database: PDB / ID: 6xaz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the PR domain from human PRDM5 | ||||||
Components | PR domain zinc finger protein 5 | ||||||
Keywords | TRANSCRIPTION / PRDM5 / TRANSFERASE | ||||||
Function / homology | Function and homology information : / DNA-binding transcription factor binding => GO:0140297 / : / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / mitotic cell cycle / regulation of gene expression ...: / DNA-binding transcription factor binding => GO:0140297 / : / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to leukemia inhibitory factor / methyltransferase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / mitotic cell cycle / regulation of gene expression / sequence-specific DNA binding / nuclear body / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mou, T.C. / Kerchner, K.M. / Sprang, S.R. / Briknarova, K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure of the PR domain from human PRDM5 Authors: Mou, T.C. / Kerchner, K.M. / Sprang, S.R. / Briknarova, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xaz.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xaz.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/6xaz ftp://data.pdbj.org/pub/pdb/validation_reports/xa/6xaz | HTTPS FTP |
---|
-Related structure data
Related structure data | 4c1qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14927.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM5, PFM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NQX1, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.67 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate pH 6.5, 2.0 M ammonium sulfate, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.19 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23.83 Å / Num. obs: 31092 / % possible obs: 98.1 % / Redundancy: 9.8 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2929 / Rsym value: 0.49 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C1Q Resolution: 1.7→23.83 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.36 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→23.83 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å
|