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Yorodumi- PDB-2r3v: The Biochemical and Structural Basis for Feedback Inhibition of M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r3v | ||||||
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Title | The Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism | ||||||
Components | Mevalonate kinase | ||||||
Keywords | TRANSFERASE / Mevalonate Kinase / Farnesyl thiodiphophate / ATP-binding / Cataract / Cholesterol biosynthesis / Cytoplasm / Disease mutation / Lipid synthesis / Nucleotide-binding / Peroxisome / Polymorphism / Steroid biosynthesis / Sterol biosynthesis | ||||||
Function / homology | Function and homology information mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / negative regulation of inflammatory response / peroxisome ...mevalonate kinase / mevalonate kinase activity / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / negative regulation of inflammatory response / peroxisome / intracellular membrane-bounded organelle / magnesium ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Fu, Z. / Voynova, N.E. / Miziorko, H.M. / Kim, J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism. Authors: Fu, Z. / Voynova, N.E. / Herdendorf, T.J. / Miziorko, H.M. / Kim, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r3v.cif.gz | 297 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r3v.ent.gz | 242 KB | Display | PDB format |
PDBx/mmJSON format | 2r3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/2r3v ftp://data.pdbj.org/pub/pdb/validation_reports/r3/2r3v | HTTPS FTP |
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-Related structure data
Related structure data | 2r42C 1kvkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42497.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MVK / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 DE3 / References: UniProt: Q03426, mevalonate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: MES buffer, PEG5k MME, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 25, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.37 Å / Num. obs: 46347 / % possible obs: 84.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.18 / % possible all: 44.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1kvk Resolution: 2.5→29.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 404877.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.6162 Å2 / ksol: 0.269456 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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