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- PDB-1ude: Crystal structure of the Inorganic pyrophosphatase from the hyper... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ude | ||||||
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Title | Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 | ||||||
![]() | Inorganic pyrophosphatase | ||||||
![]() | HYDROLASE / inorganic pyrophosphatase X-ray crystallographic analysis | ||||||
Function / homology | ![]() inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, B. / Gao, R. / Zhou, W. / Bartlam, M. / Rao, Z. | ||||||
![]() | ![]() Title: Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii. Authors: Liu, B. / Bartlam, M. / Gao, R. / Zhou, W. / Pang, H. / Liu, Y. / Feng, Y. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 482.4 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit by crystallographic quadratic operations |
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Components
#1: Protein | Mass: 22803.168 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.1 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, Na Acetete, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5.2 / PH range high: 5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→50 Å / Num. obs: 17030 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.93 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.66→2.9 Å / % possible all: 98 |
Reflection | *PLUS Num. measured all: 118041 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 4.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: inorganic pyrophosphatase Sulfolobus acidocaldarius (S-PPase)
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Refinement step | Cycle: LAST / Resolution: 2.66→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.83 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Refinement | *PLUS Num. reflection obs: 117986 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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