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- PDB-3lgz: Crystal structure of dehydrosqualene synthase Y129A from S. aureu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lgz | ||||||
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Title | Crystal structure of dehydrosqualene synthase Y129A from S. aureus complexed with presqualene pyrophosphate | ||||||
![]() | Dehydrosqualene synthase | ||||||
![]() | TRANSFERASE / C30 carotenoid / virulence factor / presqualene diphosphate / PSPP | ||||||
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, Y.-L. / Liu, C.-I. / 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. / 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 | ![]() | 75.9 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 699.2 KB | Display | ![]() |
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Full document | ![]() | 706.5 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3acwC ![]() 3acxC ![]() 3acyC ![]() 3adzC ![]() 3ae0C ![]() 3nprC ![]() 3nriC ![]() 2zcp 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: 34695.402 Da / Num. of mol.: 1 / Mutation: Y129A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A9JQL9, Transferases; Transferring alkyl or aryl groups, other than methyl groups | ||
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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: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 298 K / 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: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2009 Details: SI(111) DOUBLE CRYSTAL MONOCHROMETER. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETR |
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: 2.4→30 Å / Num. obs: 13306 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZCP ![]() 2zcp Resolution: 2.41→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.89 / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.303 / 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: 42.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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