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- PDB-3npr: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3npr | ||||||
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Title | Crystal structure of the C(30) carotenoid dehydrosqualene synthase from S. aureus complexed with Presqualene diphosphate (PSPP) | ||||||
![]() | Dehydrosqualene synthase | ||||||
![]() | TRANSFERASE / dehydrosqualene synthase / CrtM / presqualene diphosphate / PSPP / virulence factor / carotenoid | ||||||
Function / homology | ![]() 4,4'-diapophytoene synthase / 15-cis-phytoene synthase activity / geranylgeranyl-diphosphate geranylgeranyltransferase activity / carotenoid biosynthetic process / farnesyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, F.-Y. / Liu, C.-I. / Liu, Y.-L. / Wang, K. / Zhang, Y. / Oldfield, E. | ||||||
![]() | ![]() Title: Mechanism of action and inhibition of dehydrosqualene synthase. Authors: Lin, F.Y. / Liu, C.I. / Liu, Y.L. / Zhang, Y. / Wang, K. / Jeng, W.Y. / Ko, T.P. / Cao, R. / Wang, A.H. / Oldfield, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.6 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726 KB | Display | ![]() |
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Full document | ![]() | 731.6 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3acwC ![]() 3acxC ![]() 3acyC ![]() 3adzC ![]() 3ae0C ![]() 3lgzC ![]() 3nriC ![]() 2zcoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34787.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-PS7 / {( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 23228 / Num. obs: 21778 / % possible obs: 97.06 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB enry 2ZCO Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.337 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.206 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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