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- PDB-1kvk: The Structure of Binary complex between a Mammalian Mevalonate Ki... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kvk | ||||||
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Title | The Structure of Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease | ||||||
![]() | mevalonate kinase | ||||||
![]() | TRANSFERASE / RMK / ATP / GHMP | ||||||
Function / homology | ![]() Cholesterol biosynthesis / isoprenoid metabolic process / mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol metabolic process / isoprenoid biosynthetic process / sequence-specific mRNA binding / cholesterol biosynthetic process ...Cholesterol biosynthesis / isoprenoid metabolic process / mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol metabolic process / isoprenoid biosynthetic process / sequence-specific mRNA binding / cholesterol biosynthetic process / negative regulation of inflammatory response / peroxisome / negative regulation of translation / mRNA binding / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fu, Z. / Wang, M. / Potter, D. / Mizioko, H.M. / Kim, J.J. | ||||||
![]() | ![]() Title: The Structure of a Binary complex between a Mammalian Mevalonate Kinase and ATP: Insights into the Reaction Mechanism and Human Inherited Disease Authors: Fu, Z. / Wang, M. / Potter, D. / Mizioko, H.M. / Kim, J.J. #1: ![]() Title: Structure and Mechanism of Homoserine Kinase: Prototype for the GHMP Kinase Superfamily Authors: Zhou, T. / Daugherty, M. / Grishin, N.V. / Osterman, A.L. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42032.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Hepes, MgCl2, ATP, PEG-5KMME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→65.55 Å / Num. all: 14200 / Num. obs: 14200 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 32 / Limit h min: 0 / Limit k max: 49 / Limit k min: 0 / Limit l max: 16 / Limit l min: 0 / Observed criterion F max: 282198.29 / Observed criterion F min: 0.55 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 76.9 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 14000 / Num. measured all: 30833 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 77.8 % / Num. unique obs: 1011 / Num. measured obs: 2653 / Rmerge(I) obs: 0.305 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 48.1123 Å2 / ksol: 0.301427 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.5 Å2 / Biso mean: 43.09 Å2 / Biso min: 9.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→65.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 60 Å / Num. reflection obs: 14000 / % reflection Rfree: 8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.47 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.331 / Num. reflection Rwork: 1011 / Rfactor obs: 0.33 |