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Yorodumi- PDB-6mdf: Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mdf | ||||||
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Title | Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound | ||||||
Components | Mevalonate kinase | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / ergosterol biosynthetic process / cholesterol biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Miller, B.R. / Kung, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: PLoS ONE / Year: 2018 Title: Structural insight into substrate and product binding in an archaeal mevalonate kinase. Authors: Miller, B.R. / Kung, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mdf.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mdf.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mdf_validation.pdf.gz | 933.3 KB | Display | wwPDB validaton report |
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Full document | 6mdf_full_validation.pdf.gz | 945.1 KB | Display | |
Data in XML | 6mdf_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 6mdf_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/6mdf ftp://data.pdbj.org/pub/pdb/validation_reports/md/6mdf | HTTPS FTP |
-Related structure data
Related structure data | 6mdeC 4hacS 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
#1: Protein | Mass: 31637.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: mvk, MM_1762 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PW39, mevalonate kinase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 2.37 Å3/Da / Density % sol: 48.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Bis-Tris, pH 5.5, 200-300 mM sodium potassium tartrate, 15-25% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→51.92 Å / Num. obs: 22260 / % possible obs: 96.95 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1031 / Net I/σ(I): 8.73 |
Reflection shell | Resolution: 2.46→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3752 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 2135 / CC1/2: 0.843 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4HAC Resolution: 2.46→51.92 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→51.92 Å
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Refine LS restraints |
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LS refinement shell |
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