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Open data
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Basic information
Entry | Database: PDB / ID: 6e2u | ||||||
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Title | MDDEF in complex with MVAPP, AMPPCP and Magnesium | ||||||
![]() | Mevalonate diphosphate decarboxylase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stauffacher, C.V. / Chen, C.-L. | ||||||
![]() | ![]() Title: Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase. Authors: Chen, C.L. / Paul, L.N. / Mermoud, J.C. / Steussy, C.N. / Stauffacher, C.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 | ![]() | 137.6 KB | Display | ![]() |
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PDB format | ![]() | 104.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6e2sC ![]() 6e2tC ![]() 6e2vC ![]() 6e2wC ![]() 6e2yC ![]() 5v2lS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39276.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9FD68, ![]() |
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#2: Chemical | ChemComp-DP6 / ( |
#3: Chemical | ChemComp-ACP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM MgCl2 and 50 mM ...Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM MgCl2 and 50 mM sodium acetate, pH 4.6; Crystals were soaked with MVAPP, followed by AMPPCP. Then condensation was conducted at 30 % PEG 3350, 15% PEG 400, 5 mM MgCl2, 50 mM sodium acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.045→30 Å / Num. obs: 23332 / % possible obs: 96.6 % / Redundancy: 5.1 % / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2246 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5V2L Resolution: 2.05→28.83 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→28.83 Å
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Refine LS restraints |
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LS refinement shell |
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