[English] 日本語
Yorodumi- PDB-4du7: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4du7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with substrate mevalonate diphosphate | ||||||
Components | Mevalonate diphosphate decarboxylase | ||||||
Keywords | LYASE / GHMP Kinase Family | ||||||
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: 2.201 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4du7.cif.gz | 143 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4du7.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 4du7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4du7_validation.pdf.gz | 999.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4du7_full_validation.pdf.gz | 1004.7 KB | Display | |
Data in XML | 4du7_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4du7_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/4du7 ftp://data.pdbj.org/pub/pdb/validation_reports/du/4du7 | HTTPS FTP |
-Related structure data
Related structure data | 4dptC 4dpuC 4dpwC 4dpxC 4dpyC 4du8C 3qt5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 | #3: Chemical | ChemComp-FMT / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 31892 / Num. obs: 30297 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.2→2.2716 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.04 / % possible all: 88 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QT5 Resolution: 2.201→31.261 Å / Occupancy max: 1 / Occupancy min: 0.69 / FOM work R set: 0.8095 / SU ML: 0.28 / σ(F): 0 / Phase error: 25.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.724 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.52 Å2 / Biso mean: 34.9367 Å2 / Biso min: 17.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.201→31.261 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
|