+
Open data
-
Basic information
Entry | Database: PDB / ID: 1i40 | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF INORGANIC PYROPHOSPHATASE | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | HYDROLASE / INORGANIC PYROPHOSPHATASE | ||||||
Function / homology | ![]() inorganic triphosphate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Samygina, V.R. / Popov, A.N. / Lamzin, V.S. / Avaeva, S.M. | ||||||
![]() | ![]() Title: The structures of Escherichia coli inorganic pyrophosphatase complexed with Ca(2+) or CaPP(i) at atomic resolution and their mechanistic implications. Authors: Samygina, V.R. / Popov, A.N. / Rodina, E.V. / Vorobyeva, N.N. / Lamzin, V.S. / Polyakov, K.M. / Kurilova, S.A. / Nazarova, T.I. / Avaeva, S.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -y, x-y, z and y-x, -x, z and y, x, -z and x-y, -y, -z and -x, y-x, -z. |
-
Components
#1: Protein | Mass: 19585.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.906 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→20 Å / Num. all: 662283 / Num. obs: 79833 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 2.3 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.05→1.06 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2639 / Rsym value: 47 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 1.1 Å / Num. measured all: 662283 |
Reflection shell | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 1.12 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 1324 / Occupancy sum non hydrogen: 1592 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→12 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|