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- PDB-1qez: SULFOLOBUS ACIDOCALDARIUS INORGANIC PYROPHOSPHATASE: AN ARCHAEL P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qez | ||||||
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Title | SULFOLOBUS ACIDOCALDARIUS INORGANIC PYROPHOSPHATASE: AN ARCHAEL PYROPHOSPHATASE. | ||||||
![]() | PROTEIN (INORGANIC PYROPHOSPHATASE) | ||||||
![]() | HYDROLASE / INORGANIC PYROPHOSPHATASE / THERMOSTABILITY / MAGNESIUM | ||||||
Function / homology | ![]() inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Leppanen, V.-M. / Nummelin, H. / Hansen, T. / Lahti, R. / Schafer, G. / Goldman, A. | ||||||
![]() | ![]() Title: Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase. Authors: Leppanen, V.M. / Nummelin, H. / Hansen, T. / Lahti, R. / Schafer, G. / Goldman, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.4 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.8 KB | Display | ![]() |
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Full document | ![]() | 478.7 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 48.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2prdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19402.945 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Cellular location: CYTOPLASM / Plasmid: PET-3A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: ![]() ![]() #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: 3.12 Å3/Da / Density % sol: 60.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 4% PEG-8000, 0.2M MGCL2, 0.1M TRIS/HCL PH8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 26 ℃ / Method: vapor diffusion / Details: protein solution is mixed 2:1 with well solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 38004 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.091 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.28 / % possible all: 62.2 |
Reflection | *PLUS Num. measured all: 256303 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 62.2 % / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRD Resolution: 2.7→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 157938.29 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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