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Yorodumi- PDB-3vjd: Crystal structure of the Y248A mutant of C(30) carotenoid dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vjd | ||||||
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Title | Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus | ||||||
Components | Dehydrosqualene synthase4,4'-Diapophytoene synthase | ||||||
Keywords | TRANSFERASE / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation | ||||||
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: 1.48 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Wang, A.H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Ko, T.P. / Wang, A.H.J. #1: Journal: Science / Year: 2008 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.J. / Oldfield, E. #2: Journal: J.Med.Chem. / Year: 2009 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.J. / Oldfield, E. #3: 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.J. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vjd.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vjd.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/3vjd ftp://data.pdbj.org/pub/pdb/validation_reports/vj/3vjd | HTTPS FTP |
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-Related structure data
Related structure data | 3vj8C 3vj9C 3vjaC 3vjbC 3vjcC 3vjeC 2zcoS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34695.402 Da / Num. of mol.: 1 / Mutation: Y248A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ATCC 27659 / Gene: crtM / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) pLysS References: UniProt: A9JQL9, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Chemical | ChemComp-TLA / |
#3: 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: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.12-0.58M potassium sodium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2010 / Details: HORIZONTAL FOCUSING MIRROR |
Radiation | Monochromator: LN2-Cooled Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. all: 55854 / Num. obs: 55684 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5523 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZCO Resolution: 1.48→27.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.145 / SU ML: 0.038 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / 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: 25.609 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.56 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 16.5671 Å / Origin y: 53.7061 Å / Origin z: 36.9076 Å
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Refinement TLS group |
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