+Open data
-Basic information
Entry | Database: PDB / ID: 2qjc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a putative diadenosine tetraphosphatase | ||||||
Components | Diadenosine tetraphosphatase, putative | ||||||
Keywords | 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 | Function and homology information bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / protein serine/threonine phosphatase activity / protein dephosphorylation / hydrolase activity Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Sugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qjc.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qjc.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjc ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjc | 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 (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28536.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: GUTat10.1 / Gene: Tb927.8.8040 / Plasmid: pSGX3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q57U41, bis(5'-nucleosyl)-tetraphosphatase (symmetrical) | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.17 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.05→49.4 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 183986.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber 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.
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.5085 Å2 / ksol: 0.381149 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→49.4 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.13 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|