+Open data
-Basic information
Entry | Database: PDB / ID: 6e2v | ||||||
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Title | MDDEF in complex with MVAPP, ADPBeF3 and magnesium | ||||||
Components | Mevalonate diphosphate decarboxylase | ||||||
Keywords | LYASE / Mevalonate diphosphate decarboxylase | ||||||
Function / homology | Function and homology information diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Stauffacher, C.V. / Chen, C.-L. | ||||||
Citation | Journal: Nat Commun / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e2v.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e2v.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 6e2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/6e2v ftp://data.pdbj.org/pub/pdb/validation_reports/e2/6e2v | HTTPS FTP |
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-Related structure data
Related structure data | 6e2sC 6e2tC 6e2uC 6e2wC 6e2yC 5v2lS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Enterococcus faecalis (bacteria) / Gene: mvaD, B6S42_02310 / Production host: Escherichia coli (E. coli) References: UniProt: Q9FD68, diphosphomevalonate decarboxylase |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | #3: Chemical | ChemComp-DP6 / ( | #4: Chemical | ChemComp-BEF / | #5: Chemical | ChemComp-ADP / | #6: 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: 2.28 Å3/Da / Density % sol: 46.07 % |
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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 ADPBeF3. 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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 22880 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rpim(I) all: 0.029 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2229 / CC1/2: 0.832 / Rpim(I) all: 0.289 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V2L Resolution: 2.1→28.703 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→28.703 Å
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Refine LS restraints |
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LS refinement shell |
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