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Yorodumi- PDB-3lgz: Crystal structure of dehydrosqualene synthase Y129A from S. aureu... -
+Open data
-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 | ||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | ||||||
Keywords | TRANSFERASE / C30 carotenoid / virulence factor / presqualene diphosphate / PSPP | ||||||
Function / homology | Function and homology information 4,4'-diapophytoene synthase / carotenoid biosynthetic process / farnesyltranstransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Lin, F.-Y. / Liu, Y.-L. / Liu, C.-I. / Wang, A.H.J. / Oldfield, E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lgz.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lgz.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 3lgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/3lgz ftp://data.pdbj.org/pub/pdb/validation_reports/lg/3lgz | HTTPS FTP |
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-Related structure data
Related structure data | 3acwC 3acxC 3acyC 3adzC 3ae0C 3nprC 3nriC 2zcp 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: 34695.402 Da / Num. of mol.: 1 / Mutation: Y129A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: crtm / Plasmid: PET-32 XA/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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