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Yorodumi- PDB-3acx: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3acx | ||||||
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Title | Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with BPH-673 | ||||||
Components | Dehydrosqualene synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Transferase / Head-to-head condensation / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / 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.J. / Oldfield, E. #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. / 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. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3acx.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3acx.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 3acx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3acx_validation.pdf.gz | 658.5 KB | Display | wwPDB validaton report |
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Full document | 3acx_full_validation.pdf.gz | 662.2 KB | Display | |
Data in XML | 3acx_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3acx_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/3acx ftp://data.pdbj.org/pub/pdb/validation_reports/ac/3acx | HTTPS FTP |
-Related structure data
Related structure data | 3acwC 3acyC 3adzC 3ae0C 3lgzC 3nprC 3nriC 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
#1: Protein | Mass: 34787.496 Da / Num. of mol.: 1 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-673 / |
#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: 2.44 Å3/Da / Density % sol: 49.59 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2008 / Details: Vertically Focusing Mirror |
Radiation | Monochromator: Horizontally Focusing Single Crystal Si(111) Bent Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97315 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→30 Å / Num. all: 82023 / Num. obs: 81916 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 66.3 |
Reflection shell | Resolution: 1.31→1.36 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 9.7 / Num. unique all: 8101 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZCO Resolution: 1.31→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.231 / SU ML: 0.024 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / 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: 12.605 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.381 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 55.5295 Å / Origin y: 12.1679 Å / Origin z: 52.0644 Å
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