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- PDB-1j3b: Crystal structure of ATP-dependent phosphoenolpyruvate carboxykin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j3b | ||||||
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Title | Crystal structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 | ||||||
![]() | ATP-dependent phosphoenolpyruvate carboxykinase | ||||||
![]() | TRANSFERASE / phosphoenolpyruvate carboxykinase / adenosine triphosphate / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugahara, M. / Miyano, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability. Authors: Sugahara, M. / Ohshima, N. / Ukita, Y. / Sugahara, M. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.7 KB | Display | ![]() |
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PDB format | ![]() | 182.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xkvC ![]() 1oenS S: Starting model for refinement 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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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit. |
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Components
#1: Protein | Mass: 59387.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.25 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.3 Details: potassium phosphate, sodium phosphate, pH 6.3, MICROBATCH, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 99163 / Num. obs: 99163 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.32 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.07 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 4.19 / Num. unique all: 9804 / Rsym value: 0.675 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 726185 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1OEN Resolution: 2→36.1 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.015
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Refinement | *PLUS Lowest resolution: 40 Å / Num. reflection obs: 98955 / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / Rfactor Rwork: 0.29 |