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- PDB-7lnv: Apo Structure of Isopentenyl Phosphate Kinase from Candidatus met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lnv | ||||||
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Title | Apo Structure of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus | ||||||
![]() | Isopentenyl phosphate kinase | ||||||
![]() | TRANSFERASE / Phosphotransferase ATP Biocatalysis Isoprenoids Enzyme Promiscuity | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / terpenoid biosynthetic process / kinase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomas, L.M. / Singh, S. / Scull, E.M. / Bourne, C.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus . Authors: Johnson, B.P. / Kumar, V. / Scull, E.M. / Thomas, L.M. / Bourne, C.R. / 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 | ![]() | 191.4 KB | Display | ![]() |
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PDB format | ![]() | 122 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478 KB | Display | ![]() |
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Full document | ![]() | 486 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lntC ![]() 7lnuC ![]() 7lnwC ![]() 7lnxC ![]() 7n9dC ![]() 3lkkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30533.225 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BKD89_07040 / Production host: ![]() ![]() References: UniProt: A0A3G3II74, isopentenyl phosphate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: 0.2 M Sodium Malonate pH 7.0, 20% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 25, 2016 / Details: Osmic Veri Max mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 44070 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.89 Å2 / CC1/2: 0.997 / Χ2: 0.982 / Net I/σ(I): 9.91 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 2159 / CC1/2: 0.552 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LKK Resolution: 2.2→37.29 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1766 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: 39.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.29 Å
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Refine LS restraints |
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LS refinement shell |
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