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Yorodumi- PDB-3fdf: Crystal structure of the serine phosphatase of RNA polymerase II ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fdf | ||||||
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Title | Crystal structure of the serine phosphatase of RNA polymerase II CTD (SSU72 superfamily) from Drosophila melanogaster. Orthorhombic crystal form. Northeast Structural Genomics Consortium target FR253. | ||||||
Components | FR253 | ||||||
Keywords | structural genomics / unknown function / FR253 phosphatase CTD serine NESG structure Drosofila melanogaster / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
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 / MAD / Resolution: 3.2 Å | ||||||
Authors | Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Forouhar, F. / Chinag, Y. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Forouhar, F. / Chinag, Y. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Orthorombic crystal structure of serine phosphatase of rna polymerase ii ctd from fly drosofila melanogaster. northeast structural genomics consortium target fr253. Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Forouhar, F. / Chinag, Y. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fdf.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fdf.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/3fdf ftp://data.pdbj.org/pub/pdb/validation_reports/fd/3fdf | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Details | monomer |
-Components
#1: Protein | Mass: 23326.709 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: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q9VWE4 |
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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: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: PEG3350 18%, benzamidine 2%, KCl 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97926, 0.97949, 0.96791 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2006 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→30 Å / Num. obs: 28511 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 26.1 | ||||||||||||
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→19.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 228217.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.153 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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