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Yorodumi- PDB-3qt6: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qt6 | ||||||
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Title | Crystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor DPGP | ||||||
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: 2.047 Å | ||||||
Authors | Barta, M.L. / Skaff, A.D. / McWhorter, W.J. / Miziorko, H.M. / Geisbrecht, B.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis. Authors: Barta, M.L. / Skaff, D.A. / McWhorter, W.J. / Herdendorf, T.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 | 3qt6.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qt6.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qt6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3qt6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3qt6_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 3qt6_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/3qt6 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/3qt6 | HTTPS FTP |
-Related structure data
Related structure data | 3qt5SC 3qt7C 3qt8C 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: 36870.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: mvaD / Production host: Escherichia coli (E. coli) References: UniProt: Q9FD73, diphosphomevalonate decarboxylase #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 44.05 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2011 |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.047→49.34 Å / Num. all: 41214 / Num. obs: 41213 / % possible obs: 98.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4081 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QT5 Resolution: 2.047→29.601 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.897 Å2 / ksol: 0.352 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.047→29.601 Å
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Refine LS restraints |
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LS refinement shell |
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