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- PDB-8u0k: Crystal structure of isopentenyl phosphate kinase from Thermococc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u0k | ||||||
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Title | Crystal structure of isopentenyl phosphate kinase from Thermococcus paralvinellae bound to DMAP and ADP | ||||||
![]() | Isopentenyl phosphate kinase | ||||||
![]() | TRANSFERASE / Alternate Mevalonate pathway IPK Amino acid kinase isoprenoids | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, S. / Thomas, L.M. / Johnson, B.P. / Brown, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Ternary complexes of isopentenyl phosphate kinase from Thermococcus paralvinellae reveal molecular determinants of non-natural substrate specificity. Authors: Johnson, B.P. / Mandal, P.S. / Brown, S.M. / Thomas, L.M. / Singh, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.6 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u0lC ![]() 8u0mC ![]() 8u0nC ![]() 7lntS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31962.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.13 M magnesium formate, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.74 Å / Num. obs: 22535 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 54.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.126 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 1.277 / Num. unique obs: 2301 / CC1/2: 0.463 / Rrim(I) all: 1.579 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7LNT Resolution: 2.5→38.74 Å / SU ML: 0.378 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6677 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38.74 Å
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Refine LS restraints |
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LS refinement shell |
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