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- PDB-6e2y: MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data -
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Open data
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Basic information
Entry | Database: PDB / ID: 6e2y | ||||||
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Title | MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data | ||||||
![]() | Mevalonate diphosphate decarboxylase | ||||||
![]() | LYASE / Mevalonate diphosphate decarboxylase | ||||||
Function / homology | ![]() diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / metal ion binding / cytosol 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 | ![]() | 140.3 KB | Display | ![]() |
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PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016.9 KB | Display | ![]() |
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Full document | ![]() | 1017.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e2sC ![]() 6e2tC ![]() 6e2uC ![]() 6e2vC ![]() 6e2wC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39276.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9FD68, diphosphomevalonate decarboxylase |
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-Non-polymers , 5 types, 147 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/DP6.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/DP6.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-DP6 / ( | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.19 % |
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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 CoCl2 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 CoCl2 and 50 mM sodium acetate, pH 4.6; Crystals were soaked with MVAPP (200 micromole), followed by ATPgS (200 micromole). Then condensation was conducted at 30 % PEG 3350, 15% PEG 400, 5 mM CoCl2, 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: Mar 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→30 Å / Num. obs: 15794 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rpim(I) all: 0.022 / Net I/σ(I): 40 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1541 / CC1/2: 0.92 / Rpim(I) all: 0.144 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5V2L Resolution: 2.34→26.612 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→26.612 Å
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Refine LS restraints |
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LS refinement shell |
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