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- PDB-4du8: Crystal structure of Staphylococcus epidermidis D283A mevalonate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4du8 | ||||||
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Title | Crystal structure of Staphylococcus epidermidis D283A mevalonate diphosphate decarboxylase complexed with inhibitor DPGP | ||||||
![]() | Mevalonate diphosphate decarboxylase | ||||||
![]() | LYASE/LYASE INHIBITOR / GHMP Kinase Family / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barta, M.L. / McWhorter, W.J. / Geisbrecht, B.V. | ||||||
![]() | ![]() Title: Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase. Authors: Barta, M.L. / McWhorter, W.J. / Miziorko, H.M. / Geisbrecht, B.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.1 KB | Display | ![]() |
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PDB format | ![]() | 111.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dptC ![]() 4dpuC ![]() 4dpwC ![]() 4dpxC ![]() 4dpyC ![]() 4du7C ![]() 3qt5S 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
#1: Protein | Mass: 36826.387 Da / Num. of mol.: 2 / Mutation: D283A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9FD73, diphosphomevalonate decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.25 M sodium formate, 16% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 35770 / Num. obs: 33987 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 24.79 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.1→2.1572 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.58 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QT5 Resolution: 2.1→42.629 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.8357 / SU ML: 0.26 / σ(F): 0 / Phase error: 23.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.91 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.68 Å2 / Biso mean: 27.7397 Å2 / Biso min: 10.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.629 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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