+Open data
-Basic information
Entry | Database: PDB / ID: 2hhp | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of yeast poly(A) polymerase in a closed conformation. | ||||||
Components | Poly(A) polymerase | ||||||
Keywords | TRANSFERASE / template-independent RNA polymerase | ||||||
Function / homology | Function and homology information sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, poly(A)-coupled / mRNA cleavage and polyadenylation specificity factor complex / poly(A) RNA polymerase activity / polynucleotide adenylyltransferase / mRNA 3'-end processing / magnesium ion binding / RNA binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bohm, A. / Toth, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase. Authors: Balbo, P.B. / Toth, J. / Bohm, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hhp.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hhp.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 2hhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hhp_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2hhp_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 2hhp_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 2hhp_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hhp ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hhp | HTTPS FTP |
-Related structure data
Related structure data | 2o1pC 1fa0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | These crystals contain one molecule in the ASU, and the protein functions as a monomer. |
-Components
#1: Protein | Mass: 60564.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PAP1 / Production host: Escherichia coli (E. coli) References: UniProt: P29468, polynucleotide adenylyltransferase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: The crystals were grown by combining the protein at 20mg/ml with an equal volume of 20% isopropanol, 20% Peg 4000, 100mM Citrate pH 5.6, and 0.1% beta mercaptoethanol, and then leaving the ...Details: The crystals were grown by combining the protein at 20mg/ml with an equal volume of 20% isopropanol, 20% Peg 4000, 100mM Citrate pH 5.6, and 0.1% beta mercaptoethanol, and then leaving the hanging drops for two weeks over an empty reservoir well., vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 57072 / Num. obs: 56901 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.057 / Net I/σ(I): 46 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.46 / Rsym value: 0.448 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1FA0 Resolution: 1.8→33.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.452 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.965 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|