+Open data
-Basic information
Entry | Database: PDB / ID: 3omx | ||||||
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Title | Crystal structure of Ssu72 with vanadate complex | ||||||
Components | CG14216 | ||||||
Keywords | HYDROLASE / transition state / phosphatase / low molecular weight protein tyrosine phosphatase / dephosphorylation / RNA polymerase II / Pta1 | ||||||
Function / homology | Function and homology information RNA polymerase II transcribes snRNA genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / myosin phosphatase activity / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / phosphatase activity / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3366 Å | ||||||
Authors | Zhang, Y. / Zhang, M. / Zhang, Y. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue. Authors: Zhang, Y. / Zhang, M. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3omx.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3omx.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 3omx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3omx_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 3omx_full_validation.pdf.gz | 525.7 KB | Display | |
Data in XML | 3omx_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 3omx_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/3omx ftp://data.pdbj.org/pub/pdb/validation_reports/om/3omx | HTTPS FTP |
-Related structure data
Related structure data | 3omwSC S: Starting model for refinement C: citing same article (ref.) |
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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: 22232.393 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG14216, Dmel_CG14216 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VWE4 #2: Chemical | ChemComp-VO4 / #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: 2.98 Å3/Da / Density % sol: 58.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 10% isopropanol, 14-18% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2010 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3366→48.67 Å / Num. all: 45740 / Num. obs: 45695 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.07 / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 2.3366→2.39 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.761 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OMW Resolution: 2.3366→48.656 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97 / 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 / Bsol: 62.002 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3366→48.656 Å
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Refine LS restraints |
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LS refinement shell |
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