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- PDB-6mdf: Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mdf | ||||||
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Title | Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound | ||||||
![]() | Mevalonate kinase | ||||||
![]() | TRANSFERASE / kinase | ||||||
Function / homology | ![]() mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / ergosterol biosynthetic process / cholesterol biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, B.R. / Kung, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into substrate and product binding in an archaeal mevalonate kinase. Authors: Miller, B.R. / Kung, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.1 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 933.3 KB | Display | ![]() |
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Full document | ![]() | 945.1 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mdeC ![]() 4hacS 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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Unit cell |
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Components
#1: Protein | Mass: 31637.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Bis-Tris, pH 5.5, 200-300 mM sodium potassium tartrate, 15-25% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→51.92 Å / Num. obs: 22260 / % possible obs: 96.95 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1031 / Net I/σ(I): 8.73 |
Reflection shell | Resolution: 2.46→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3752 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 2135 / CC1/2: 0.843 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4HAC Resolution: 2.46→51.92 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→51.92 Å
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Refine LS restraints |
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LS refinement shell |
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