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- PDB-4du7: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4du7 | ||||||
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Title | Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with substrate mevalonate diphosphate | ||||||
![]() | Mevalonate diphosphate decarboxylase | ||||||
![]() | LYASE / GHMP Kinase Family | ||||||
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 | ![]() | 143 KB | Display | ![]() |
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PDB format | ![]() | 112 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 999.8 KB | Display | ![]() |
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Full document | ![]() | 1004.7 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dptC ![]() 4dpuC ![]() 4dpwC ![]() 4dpxC ![]() 4dpyC ![]() 4du8C ![]() 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: 36870.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9FD73, diphosphomevalonate decarboxylase #2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
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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: 2.2→50 Å / Num. all: 31892 / Num. obs: 30297 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.2→2.2716 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.04 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QT5 Resolution: 2.201→31.261 Å / Occupancy max: 1 / Occupancy min: 0.69 / FOM work R set: 0.8095 / SU ML: 0.28 / σ(F): 0 / Phase error: 25.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.724 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.52 Å2 / Biso mean: 34.9367 Å2 / Biso min: 17.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.201→31.261 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: 11
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