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Open data
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Basic information
Entry | Database: PDB / ID: 2qjc | ||||||
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Title | Crystal structure of a putative diadenosine tetraphosphatase | ||||||
![]() | Diadenosine tetraphosphatase, putative | ||||||
![]() | HYDROLASE / 9095b / putative diadenosine tetraphosphatase / monomer / PSI-2 / Protein Structure Initiative / NYSGRC / Structural Genomics / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / protein serine/threonine phosphatase activity / protein dephosphorylation / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugadev, R. / Burley, S.K. / Swaminathan, S. / 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 | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 41.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 441.7 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.4 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 ![]() 2q5eC ![]() 2r0bC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28536.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q57U41, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 15002 / Num. obs: 15002 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1 / Num. unique all: 1428 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.5085 Å2 / ksol: 0.381149 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.13 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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