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- PDB-6k31: Crystal structure of pyrophosphate-dependent phosphoenolpyruvate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k31 | ||||||
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Title | Crystal structure of pyrophosphate-dependent phosphoenolpyruvate carboxykinase (PPi-PEPCK) | ||||||
![]() | AiPEPCK | ||||||
![]() | LYASE / phosphoenolpyruvate carboxykinase | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chiba, Y. / Miyakawa, T. / Tanokura, M. | ||||||
![]() | ![]() Title: Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes. Authors: Chiba, Y. / Miyakawa, T. / Shimane, Y. / Takai, K. / Tanokura, M. / Nozaki, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 441.7 KB | Display | ![]() |
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PDB format | ![]() | 364 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 74.9 KB | Display | |
Data in CIF | ![]() | 104.8 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 126997.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 400, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97887 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.12 Å / Num. obs: 91847 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.049 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 4505 / CC1/2: 0.837 / Rpim(I) all: 0.389 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.565 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→48.12 Å
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Refine LS restraints |
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