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- PDB-2q5e: Crystal structure of human carboxy-terminal domain RNA polymerase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2q5e | ||||||
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Title | Crystal structure of human carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 | ||||||
![]() | Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 | ||||||
![]() | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() RNA polymerase II CTD heptapeptide repeat phosphatase activity / XBP1(S) activates chaperone genes / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / IRE1-mediated unfolded protein response / phosphoprotein phosphatase activity / protein dephosphorylation / negative regulation of protein phosphorylation / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Structural genomics of protein phosphatases. Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 288 KB | Display | ![]() |
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PDB format | ![]() | 235.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.2 KB | Display | ![]() |
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Full document | ![]() | 531.8 KB | Display | |
Data in XML | ![]() | 52.9 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rxdC ![]() 2fh7C ![]() 2g59C ![]() 2hcmC ![]() 2hhlC ![]() 2hxpC ![]() 2hy3C ![]() 2i0oC ![]() 2i1yC ![]() 2i44C ![]() 2iq1C ![]() 2irmC ![]() 2isnC ![]() 2nv5C ![]() 2oycC ![]() 2p27C ![]() 2p4uC ![]() 2p69C ![]() 2p8eC ![]() 2pbnC ![]() 2qjcC ![]() 2r0bC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
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Components
#1: Protein | Mass: 21240.197 Da / Num. of mol.: 8 / Fragment: Residues 87-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14595, protein-serine/threonine phosphatase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 2.8 M Sodium acetate, pH 7.0, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→96.76 Å / Num. all: 72419 / Num. obs: 72419 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.51→2.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8821 / Rsym value: 0.447 / % possible all: 81.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.075 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.574 Å / Total num. of bins used: 20
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