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- PDB-3acw: 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: 3acw | ||||||
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Title | Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with BPH-651 | ||||||
![]() | Dehydrosqualene synthase![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, C.I. / Jeng, W.Y. / Wang, A.H.J. / 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.J. / Oldfield, E. #1: ![]() Title: A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Authors: Liu, C.I. / Liu, G.Y. / Song, Y. / Yin, F. / Hensler, M.E. / Jeng, W.Y. / Nizet, V. / Wang, A.H. / Oldfield, E. #2: ![]() Title: Inhibition of staphyloxanthin virulence factor biosynthesis in Staphylococcus aureus: in vitro, in vivo, and crystallographic results. Authors: Song, Y. / Liu, C.I. / Lin, F.Y. / No, J.H. / Hensler, M. / Liu, Y.L. / Jeng, W.Y. / Low, J. / Liu, G.Y. / Nizet, V. / 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 | ![]() | 143 KB | Display | ![]() |
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PDB format | ![]() | 111.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3acxC ![]() 3acyC ![]() 3adzC ![]() 3ae0C ![]() 3lgzC ![]() 3nprC ![]() 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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A9JQL9, ![]() |
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#2: Chemical | ChemComp-651 / ( |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.12-0.58M potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.63→30 Å / Num. all: 42844 / Num. obs: 42617 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4208 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2ZCO Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.547 / SU ML: 0.055 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.087 / 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: 23.937 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.718 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 55.5703 Å / Origin y: 12.4029 Å / Origin z: 51.809 Å
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