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Yorodumi- PDB-4dpt: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dpt | ||||||
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Title | Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS | ||||||
Components | Mevalonate diphosphate decarboxylase | ||||||
Keywords | LYASE/LYASE INHIBITOR / GHMP Kinase Family / LYASE-LYASE INHIBITOR complex | ||||||
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 | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å | ||||||
Authors | Barta, M.L. / McWhorter, W.J. / Geisbrecht, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dpt.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dpt.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dpt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4dpt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4dpt_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 4dpt_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/4dpt ftp://data.pdbj.org/pub/pdb/validation_reports/dp/4dpt | HTTPS FTP |
-Related structure data
Related structure data | 4dpuC 4dpwC 4dpxC 4dpyC 4du7C 4du8C 3qt5S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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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.) Staphylococcus epidermidis (bacteria) / Gene: mvaD / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9FD73, diphosphomevalonate decarboxylase #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-FM0 / ( | #4: Chemical | ChemComp-AGS / | #5: 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: 2.26 Å3/Da / Density % sol: 45.62 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2011 / Details: mirror |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 32074 / Num. obs: 30466 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 31.55 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.19→2.26 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.31 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QT5 Resolution: 2.191→28.478 Å / Occupancy max: 1 / Occupancy min: 0.72 / FOM work R set: 0.8159 / SU ML: 0.29 / σ(F): 0 / Phase error: 25.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.464 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.17 Å2 / Biso mean: 37.8373 Å2 / Biso min: 17.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.191→28.478 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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