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Yorodumi- PDB-2zy1: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zy1 | ||||||
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Title | Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with bisphosphonate BPH-830 | ||||||
Components | Dehydrosqualene synthase | ||||||
Keywords | TRANSFERASE / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation / Inhibitor | ||||||
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: 1.78 Å | ||||||
Authors | Liu, C.I. / Jeng, W.Y. / Wang, A.H.J. / Oldfield, E. | ||||||
Citation | 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zy1.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zy1.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/2zy1 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/2zy1 | HTTPS FTP |
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-Related structure data
Related structure data | 2zcoS S: Starting model for refinement |
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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: 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-830 / |
#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: 2.43 Å3/Da / Density % sol: 49.29 % |
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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: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. all: 32866 / Num. obs: 32804 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 51.7 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3224 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZCO Resolution: 1.78→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å / Rfactor Rfree error: 0.008
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