+Open data
-Basic information
Entry | Database: PDB / ID: 3v46 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Yeast Cdc73 C-Terminal Domain | ||||||
Components | Cell division control protein 73 | ||||||
Keywords | TRANSCRIPTION / Ras-like fold / non-GTP binding / Protein Interaction Surface / Transcription Elongation Factor | ||||||
Function / homology | Function and homology information positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / negative regulation of DNA recombination / mRNA 3'-end processing / : / RNA polymerase II complex binding / transcription elongation by RNA polymerase I / transcription elongation by RNA polymerase II ...positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / negative regulation of DNA recombination / mRNA 3'-end processing / : / RNA polymerase II complex binding / transcription elongation by RNA polymerase I / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / chromatin binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.549 Å | ||||||
Authors | Amrich, C.G. / VanDemark, A.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Cdc73 subunit of Paf1 complex contains C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin. Authors: Amrich, C.G. / Davis, C.P. / Rogal, W.P. / Shirra, M.K. / Heroux, A. / Gardner, R.G. / Arndt, K.M. / VanDemark, A.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3v46.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3v46.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 3v46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/3v46 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v46 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20065.814 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain residues 230-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC73, YLR418C / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: Q06697 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: PEG 8000, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 12.3 % / Av σ(I) over netI: 58.1 / Number: 230812 / Rmerge(I) obs: 0.064 / Χ2: 0.87 / D res high: 1.78 Å / D res low: 50 Å / Num. obs: 18777 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.549→50 Å / Num. all: 28216 / Num. obs: 28111 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.054 / Χ2: 2.038 / Net I/σ(I): 17.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: SAD | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing MAD set site |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.549→37.706 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8784 / SU ML: 0.16 / σ(F): 0.18 / Phase error: 18.18 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.378 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.97 Å2 / Biso mean: 31.8662 Å2 / Biso min: 11.58 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.549→37.706 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|